"It's never an easy decision to make a change," Andy MacPhail said. "Ruben has had a direct impact on some of the best years in the team's history. He helped to create some great memories for Phillies fans with his accomplishments, but in order to return to a top-contending club, we believe this is the right thing to do as we continue the rebuilding process."
The Phillies have the worst record in the majors at 54-86 and will miss the postseason for the fourth straight year after winning five consecutive NL East titles. They're on pace to lose 100 games for the first time since going 47-107 in 1961 and their .386 winning percentage is the lowest in 43 years.
Amaro replaced Pat Gillick, who retired after the Phillies won the 2008 World Series and took over as team president last year. Amaro previously served 10 years as assistant GM.
Amaro rose from team batboy in 1980-83 to playing for the Phillies for five seasons in the 1990s. He guided the Phillies to the 2009 NL pennant and three division titles.
"The Phillies ownership fully supports Andy's decision not to extend Ruben Amaro's contract," team co-owner John Middleton said. "As a group, we have tremendous respect for Ruben, who has been a significant contributor to this organization. This decision is about taking the club in a new direction and that will be facilitated by new leadership."
Manager Ryne Sandberg resigned in June after going 119-159 over parts of three seasons leading Philadelphia. MacPhail was hired a week later to replace Gillick as president after the season.
Amaro wasn't afraid of making big moves during his tenure. He acquired Cliff Lee, Roy Halladay, Roy Oswalt and Hunter Pence in trades. He also traded Lee and signed him a year later in free agency. Amaro has engineered several trades during Philadelphia's rebuilding process, including dealing ace Cole Hamels to Texas and 2007 NL MVP Jimmy Rollins and six-time All-Star Chase Utley to the Dodgers.
The Detroit Tigers, Seattle Mariners, Boston Red Sox, Milwaukee Brewers and Los Angeles Angels also have made GM changes this season.