The agreement kicks in at the start of the 2008-09 season. The 22-year-old will make $942,400 this season after earning $471,200 last year.
Michalek recorded 66 points (26-40) and was a plus-17 in 78 games in 2006-07, his second full NHL campaign. He ranked second on the Sharks with a plus-17 rating and tied for fourth in the NHL with nine game-winning goals.
The Czech native picked up 35 points (17-18) in 81 games as a rookie.
"Milan defines what a multi-dimensional player should be," general manager Doug Wilson said in a statement. "He has size, speed, strength, skill and the drive to not only play, but excel in both ends of the ice."