The 11th-ranked Canadian, the runner-up at Wimbledon last year, announced his withdrawal from this season's last Grand Slam tournament on Instagram last night.
Raonic says he had "portions of the bone that have been causing the discomfort" removed.
The U.S. Open starts Monday.
Raonic joins 12-time major champion Novak Djokovic, 2016 U.S. Open champion Stan Wawrinka and 2014 finalist Kei Nishikori in missing the tournament because of injuries.
Also sitting out the action at Flushing Meadows: 23-time major champion Serena Williams, who is pregnant, and two-time Australian Open winner Victoria Azarenka, who is dealing with a custody case involving her baby son.