Nadal hasn't played a tournament since a second-round loss at Wimbledon. He withdrew from of the Olympics, where he was to have been Spain's flag bearer in the Opening Ceremonies, and a series of tournaments since because of the knee issue.
"I am very sad to announce that I am still not ready to play and have to withdraw from this year's U.S. Open in N.Y.C.," Nadal said from Spain.
"I am sorry since I always found great crowds and great support but I have to continue with my recuperation and preparation to be ready to play in the right conditions."
Nadal, 26, won the French Open, beating Novak Djokovic in four sets, but is just 2-2 since then.
In the last four years he won the 2010 U.S. Open, was the runner-up last year and a semifinalist the two previous years.
The U.S. Open, the final major tournament on the men's tennis calendar, is set for Aug. 27-Sept. 9 in New York.