Wheeldon, 33, was named City Ballet's first artist-in-residence for the 2000-01 season and began his tenure as the company's first Resident Choreographer in the 2001-02 season.
The split is reportedly amicable; Wheeldon, who wants more time to dedicate to other projects, told the Times, "There's no animosity involved at all."
Peter Martins, the balletmaster in chief, told the paper in an earlier article that Wheeldon "loved having been here. He kept saying, 'I hope that you'll invite me back.' I said, 'The door is always open to you.' I don't see this as a split. I was young once myself."
He added, however, that "The intent for me was that he would be here not temporarily, so of course I was upset. I feel we've invested in him. I like to be wise about this, and say to myself, let him go fly a little bit."
Wheeldon has created around a dozen dances for City Ballet, including Polyphonia in 2001; Morphoses and Carousel (A Dance) in 2002; Carnival of the Animals and Liturgy in 2003; Shambards in 2004 and After the Rain last year.
Wheeldon began training at the Royal Ballet at age 11 and later danced in the company. He danced with New York City Ballet from 1993 until 2000, when he turned to choreography full-time. He plans to complete two other commissions in 2008, according to the Times.