(AP Photo/Rob Griffith)
Crocker, the world record holder in the 100 fly, put up the best time in the morning preliminaries at 51.44 seconds. Phelps, his American teammate and defending world champion, was third at 51.95.
Both advanced to the evening semifinals. The much-anticipated final is Saturday night.
Phelps already has four gold medals in Melbourne, setting world records in his three individual events. He is hoping to win eight golds in all.
Crocker stands in the way.
"It's an interesting challenge," he said. "I've never had one of this magnitude before. But it's always brought the best out of me."