Ali Jackson Jr. was born in Detroit on April 3, 1976, into one of the city's jazz families. His father, Ali Muhammad Jackson (1931 to 1987), was a bassist who spent most of his working life in New York, played behind Billie Holiday, Charles Mingus, Thelonious Monk and Mary Lou Williams, and wrote "Prayer to the East," which Yusef Lateef used as the title track of his 1957 album. In the late 1940s the elder Jackson had been in a Detroit quartet called the AHJOs with pianist Roland Hanna, saxophonist Joe Alexander and his own brother, the drummer Oliver "Bops Jr." Jackson; the family was also related to Milt Jackson. He came home to Detroit in 1970 to teach at Wayne State, Oakland University and Oberlin, and he raised his sons inside the music. Ali Jr. started on drums at two and piano at five, and by his own account was on his father's gigs, playing for money, at eight.

His father passed away in 1987, when Jackson was eleven. He and his younger brother Khalil were taken in by the McKinney family, Detroit's other jazz dynasty, and his education continued under Harold, Ray, Kenneth and Bernard McKinney. He picked up lessons and mentoring from Max Roach, Milt Hinton, Donald Byrd, Betty Carter, Aretha Franklin and James Mtume, and at twelve he met Wynton Marsalis at one of those lessons and left an impression that would matter later. In Detroit in the late 1980s he made his name with the band Legacy, alongside the pianist Carlos McKinney and saxophonist J.D. Allen; they toured Europe and cut an album called With You in Mind, and the group broke up in 1997. He graduated as a music major with high honors from Cass Technical High School and went to New York on a full academic scholarship to the New School, where he studied with Max Roach and Elvin Jones and took a degree in music composition. In 1994 he was the guest soloist for the New School's Beacons of Jazz evening honoring Roach, and in 1998 he became the first recipient of Michigan's Artserv Emerging Artist award.

The New York sessions start piling up in 1996. He is on singer Sunny Sumter's Getting To Know You, taped April 10 of that year, and on the pianist Michael Heise's trio date Touchdown! for Storyville, recorded in New York on February 12, 1996 with Larry Grenadier on bass. In December he cut Russell Gunn's Gunn Fu at Sound on Sound. Then came the break, and the reversal. Marsalis hired him for the Lincoln Center orchestra in 1997 and fired him mid-job, at an NPR Making the Music session in Washington, in front of a band that included Slide Hampton, Jon Faddis and Christian McBride. Jackson bought his own train ticket back to Washington the next day, sat behind the drummer who replaced him, Herlin Riley, and watched the whole session. Seven years of other work followed: Dee Dee Bridgewater's band, caught on Live At Yoshi's in Oakland over April 23, 24 and 25, 1998; the Lionel Hampton Big Band; two years in the Mingus Big Band; the Buster Williams Quartet's Joined At The Hip, recorded May 4 and 5, 1998; James Morrison's European Sessions, cut at Bauer Studios in Ludwigsburg on March 30 and 31, 1998; and Craig Handy's Reflections In Change, made at Systems Two in Brooklyn across four days in June 1999. His first record under his own name, Groove@Jazz En Tête, came out of the Clermont-Ferrand festival on the French label Space Time in 2000, a quartet with Abraham Burton on alto, Carlos McKinney on piano and Tassili Bond on bass, with Jackson writing and arranging the whole programme.

The other New York apprenticeship ran through the basement clubs of Greenwich Village. On April 18, 1996, two weeks after his twentieth birthday, he played a piano-less, five-horn Omer Avital band at Smalls: Omer Avital on bass, Myron Walden on alto, Charles Owens and Mark Turner on tenors and Greg Tardy doubling tenor, clarinet and flute. The tapes sat for nine years and came out in 2005 as Asking No Permission: The Smalls Years Volume One. He worked with Avital again on Michael Heise's On Location (Storyville, 2000), with Avital in the bass chair. On August 29 and 30, 2003 he took a quartet into Fat Cat, a few doors from Smalls, with Marsalis on trumpet, Aaron Goldberg on piano and Robert Hurst on bass, and released the tapes as Big Brown Getdown Vol. 1. In September 2004, at Electric Lady Studio B, he made Gold Sounds with James Carter, Cyrus Chestnut and Reginald Veal, an album of Pavement songs played as gospel-inflected hard bop, on which he also sings and plays tambourine. And on January 14, 2006 he was back at Fat Cat for Avital's The Ancient Art Of Giving, with Turner, Avishai Cohen on trumpet and Goldberg.

In 2005 Marsalis gave him the drum chair of the Jazz at Lincoln Center Orchestra, and he kept it for twelve years. Jazz at Lincoln Center's own announcement, when it opened auditions for a successor on July 16, 2018, puts his tenure at 2005 through 2017 and names him the third drummer to hold the seat since the orchestra was founded in 1991. The recorded trail is long: Congo Square with Yacub Addy's Odadaa!, Ted Nash's Portrait In Seven Shades (taped September 6, 2007), The Abyssinian Mass (October 24 to 26, 2013), The Music Of John Lewis with Jon Batiste (January 19, 2013), Handful Of Keys, Una Noche Con Rubén Blades (November 16, 2014) and The Music Of Wayne Shorter (May 14 to 16, 2015). His Grammy came through the same circle but not the album usually named for it. Portrait In Seven Shades is widely reported as a Grammy winner, including on his own Wikipedia page; it was nominated. The win, Best Large Jazz Ensemble Album at the 59th ceremony in February 2017, went to the Ted Nash Big Band's Presidential Suite: Eight Variations On Freedom, recorded on September 14, 2014 with Jackson on drums and percussion. He also plays on the orchestra's Wayne Shorter programme, taped in May 2015 and issued in 2020. Alongside the big band he was Marsalis's small-group drummer on The Magic Hour, From The Plantation To The Penitentiary and He And She, on both Willie Nelson collaborations (Two Men With The Blues, taped January 12 and 13, 2007, and Here We Go Again with Norah Jones, February 9 and 10, 2009), on Play The Blues with Eric Clapton, and on the quintet meeting with Richard Galliano recorded at Marciac on August 13, 2008.

The band that has carried him since is the Yes! Trio, a genuinely co-led group with Aaron Goldberg on piano and Omer Avital on bass, drawn from the New School and Smalls circle all three had come up in. Its first record, Yes!, was cut at Systems Two in Brooklyn on December 29, 2009 and held until January 2012; it takes its title from an Avital tune the same three men had already recorded at Fat Cat, and it carries two Jackson originals. Groove Du Jour, made at Meudon outside Paris on October 29 and 30, 2018, took the Académie du Jazz's Grand Prix for album of the year for 2019, ahead of records by Avishai Cohen and Theo Croker, and Spring Sings, recorded April 21 and 22, 2022 and issued in February 2024, includes his own "Sheikh Ali." Between the first two he made his most ambitious leader date, Amalgamations, tracked at The Studio at SST in Weehawken on November 7 and 8, 2013 and released by Sunnyside on September 2, 2014, with Marsalis, JD Allen, Ted Nash, Vincent Gardner, Jon Batiste, Shedrick Mitchell, Goldberg, Eldar Djangirov, Avital, Carlos Henriquez, Phillip Keuhn and Bobby Allende passing through eleven tracks. Away from the drums he composes for dance: his own biography lists four ballets written for the choreographer Hope Boykin between 2012 and 2023, a Jazz at Lincoln Center commission called Living Grooves: A World in Jazz Rhythm, and an Alvin Ailey piece, r-Evolution, Dream. He is also, less solemnly, the voice of Duck Ellington in Penguin's Baby Loves Jazz children's series, nine volumes of which he recorded in 2006 and 2007. He has lectured on jazz at New York University, Stanford, Eastman and Columbia. His son Aziel Jackson is a professional soccer player.

Jackson is a swing-first drummer with an unusually wide historical vocabulary, which is what made him plausible in a repertory orchestra playing Ellington and Jelly Roll Morton one night and a Pavement tribute the next. Nate Chinen, writing in The New York Times in August 2009, described him as generating "a subtle but irresistible force" at the kit, an assessment that catches the thing his colleagues keep returning to: he moves a band without appearing to push it. He solos melodically across the whole surface of the set rather than in blocks, a habit traceable to Max Roach, who taught him at the New School, and to Elvin Jones, who was a close friend of his father's and whom Jackson has called an uncle. His written tribute to Jones after his death in 2004 is the clearest statement of what he values in drumming: intensity sustained over decades rather than displayed in bursts, and accessibility to people regardless of their standing. The Detroit inheritance is audible too, in the tambourine and hand percussion he brings to gospel-leaning material and in the church feel that runs through Amalgamations and Gold Sounds. He is a composer as well, credited with writing and arranging his own leader dates from the first one onward and with tunes on all three Yes! Trio albums.