
The 23-year-old Japanese won the Grand Prix events in Helsinki and Moscow in November to secure one of the six places in the final.
He will be replaced by Canadian skater Keegan Messing.
Hanyu reinjured his ankle when he fell during an official practice session for the free programme in Moscow. He then made several errors in his routine but won the event comfortably.
He had set a world record in opening short programme.
In Hanyu’s absence, the favourites in Vancouver on Dec 6-9 will be 19-year-old American Nathan Chen, who is the reigning world champion, and 20-year-old Japanese Shoma Uno, who won silver behind his compatriot in the 2018 Pyeongchang Winter Olympics.