Both McIlroy and Horizon have called in lawyers to try to settle details of an acrimonious split which comes only two years after they began working together.
The dispute follows a frustrating season when the 24-year-old from Northern Ireland has struggled for form after switching to clubs supplied by Nike in one of the biggest sponsorship deals in sport.
His new management company, Rory McIlroy Incorporated (RMI), will be headed by Donal Casey, an actuary who was already an adviser to the golfer.
His father Gerry will also be on the board of the company, with businessmen and family friend Barry Funston.
Neither side gave details of the reason for McIlroy's departure, the subject of media rumours for some months. McIlroy was believed to be unhappy with the commission that Horizon was charging for its services.
Horizon said it was disappointed that McIlroy was ending a contract that had a number of years left to run.
"Since October 2011, Horizon has achieved exceptional results for Rory in realising his commercial objectives," the company said in a statement.
"Under Horizon's management, Rory has signed some of the most lucrative endorsements in sports history."
McIlroy began the year as the hottest property in golf after signing a 10-year deal with Nike worth a reported $250 million and moving to the top of the world rankings.
However, the double major winner has slipped to sixth in the standings after his winning touch deserted him.
He is following the example of Wimbledon champion Andy Murray by taking more direct control of his business interests.
Murray and his partners have set up a management company called 77 - a reference to the numbers of years between Fred Perry winning Wimbledon and fellow Briton Murray claiming the title in July.
- Sports & Recreation
- Rory McIlroy