Bouchard is the only woman to advance to all three Grand Slam semifinals this year, a run that included an historic Wimbledon final appearance in July.
But the Westmont, Que., player is not heading to New York at her best. After her fun at Wimbledon, Bouchard lost a pair of second-round matches at tournaments in Montreal and Cincinnati.
On the men's side, Canada's Milos Raonic will be seeded fifth.
The U.S. Tennis Association followed this week's WTA rankings in announcing the seedings Wednesday.
Top-ranked Serena Williams is seeded No. 1 as she seeks her third straight U.S. Open title.
French Open runner-up Simona Halep is seeded second after reaching a career-best ranking this month. She has never advanced past the fourth round at the U.S. Open.
Wimbledon champ Petra Kvitova, who humbled Bouchard, is seeded No. 3 with third-ranked Li Na out because of a knee injury. Agnieszka Radwanska moves up to No. 4.
Five-time major champ Maria Sharapova is seeded fifth, meaning there's a chance she could face Williams in the quarterfinals. The runner-up the last two years, Victoria Azarenka, is seeded 16th after an injury-plagued season.
Venus Williams is seeded 19th.
The draw is Thursday, and the tournament starts Monday.