San Jose, which has won seven of eight, also got a goal from Bill Guerin, his 34th, for a 4-1 lead that ended the night for beleaguered goalie Kari Lehtonen with 5:31 remaining in the second period. San Jose peppered him with 23 shots.
Cheechoo made it 5-1 with 2:46 left in the period, beating Atlanta's backup Johan Hedberg for his 30th goal and second hat trick of the season, seventh career.
Atlanta, which had won eight of 10, took a 1-0 lead on Pascal Dupuis' goal at 7:53 of the first period against Vesa Toskala.
San Jose grabbed the lead later in the period on goals by Cheechoo and Michalek. Thornton, the NHL scoring champion last season, assisted on both. He has 102 points this season, the third time he has gone over the century mark, and is second to Pittsburgh's Sidney Crosby.
Cheechoo scored his second goal 12 minutes into the second period for a 3-1 lead. Thornton and Michalek drew assists.
San Jose, second in the Pacific Division, has the fifth best record in the Pacific Division, and is a virtual lock for a Western Conference playoff spot with seven games remaining.
The Thrashers, who are in good shape to make the playoffs for the first time in their seven-year history, lead the Southeast Division and are third in the Eastern Conference with seven games left.
Notes: Michalek has four goals in three games and 14 points in six contests. ... Thornton has 20 points in nine games. ... The first penalties of the game came with 5:25 left in the second period when Atlanta's Jon Sim and San Jose's Mark Bell fought. Sim injured an orbital bone and didn't return.