Third-base coach Dave Clark of Shannon was named interim manager. The Astros were 70-79 headed into Monday's home against St. Louis.
The 59-year-old Cooper was hired on Aug. 27w, 2007, to replace Phil Garner. Houston went 171-170 under Cooper, who was the bench coach under Garner between 2005-07.
Cooper became the fourth manager to get fired this season, all of them in the National League. Arizona dismissed Bob Melvin on May 7, Colorado replaced Clint Hurdle on May 29 and Washington fired Manny Acta on July 13.
Astros general manager Ed Wade said a change was needed. He said making the move now will give the Astros a chance to evaluate "other facets of our operation" heading into the offseason.
He said Clark would be considered a candidate during the search for a new manager.
Cooper did not answer calls to his cell phone and his voicemail was full.
Cooper's initial contract ran through the 2009 season and the Astros picked up his option for 2010. Houston won 86 games in 2008, a 14-game turnaround from 2007. But this season, the Astros are guaranteed their second losing record in three seasons and only the third since 1991.
Cooper was a first-time major league manager and the first black manager in Astros history. He played 11 seasons for the Milwaukee Brewers and his hiring as Houston's manager got the personal blessing of commissioner Bud Selig, who owned the Brewers from 1977-87.
Houston scored only 15 runs in a seven-game road trip last week, losing every game. The Astros are 28-46 away from Minute Maid Park this season.