Atlanta improved to 4-5-1 under general manager Don Waddell, who took over behind the bench for Curt Fraser on Dec. 26. On Tuesday, Waddell is expected to announce the hiring of Bob Hartley, who was fired as coach of the Colorado Avalanche on Dec. 18.
With two losses to Philadelphia already this season, the Thrashers jumped out to a 2-0 lead as Vyacheslav Kozlov and Heatley scored 21 seconds apart early in the first period.
After scoring just twice in his previous six contests, the 2002 Calder Trophy winner recorded his third multi-goal game of the season with just over seven minutes left in the period before netting a power-play tally midway through the second to complete the hat trick.
Jeff Odgers and Lubos Bartecko each netted his first goal of the season for Atlanta, which had not beaten the Flyers since Jan. 14, 2000.
Byron Dafoe gained the victory, making 24 saves before aggravating a groin injury late in the second period. Pasi Nurminen took over and stopped 14 of 15 shots.