The native of Coquitlam, B.C., has had injury and equipment issues since last season.
"As an athlete who takes pride in representing Canada on the world stage, I want to be able to show my best and compete at the highest level," Reynolds said in a statement. "My decision to withdraw only comes after I have given my everything in training to prepare for this event — pushing though pain and injury."
Reynolds, 24, is also pulling out of the NHK Trophy event in Japan in late November. He hopes to be ready for the upcoming Canadian Tire National Skating Championships in Kingston in January.
He has been struggling to find skates that fit properly since last season. Earlier this month, he said he had already gone through four pairs of ill-fitting skates in training this season.
Last season, he tried nine pairs, all of which were too wide for his narrow AA heel despite custom fitting.
Andrei Rogozine, a 21-year-old from Newmarket, Ont., will replace Reynolds at Skate Canada, which begins Thursday in Kelowna, B.C.