The 32-year-old has enjoyed a fine 2014, highlighted by her success at the Australian Open in January.
However, Li will skip the final grand slam of the year at Flushing Meadows - which starts next month - in order to recuperate from her injury.
Li, who will also miss the Rogers Cup and the Western and Southern Open, wrote on her official Facebook page: "I wanted to let all of my great fans know that unfortunately I am going to have to withdraw from the upcoming WTA events in Montreal and Cincinnati, as well as the US Open.
"Since March, I have been struggling with my knee and it is just not where I need it to be in order to play at the highest level.
"My medical team has advised me that I need to take some time off to rest my knee so it heels.
"I look forward to getting back on the court this fall in Wuhan and Beijing."
Li is a two-time grand slam champion, after also collecting the French Open in 2011, and has nine WTA career titles.