The Blues boss was infuriated after Jose Bosingwa and Didier Drogba were sent off in their clash at Loftus Road, and he could be punished for his remarks about referee Chris Foy
The charges relate to comments made about referee Chris Foy, who sent both Didier Drogba and Jose Bosingwa off in the first half of Chelsea’s 1-0 defeat at QPR in October.
Both challenges were viewed to be straight red cards by the referee, leading to Villas-Boas claiming the official was not in control of the game and that he was not up to the standard of a London derby.
Villas-Boas said after the game: "The ref was poor, very very poor. And it reflected in the result.
"I spoke to him at the end and I was very aggressive to him. I don't care if he's okay or not. Everyone can have a bad day, but this was not a bad day for us. It was a good day for us and a bad day for the referee."
Villas-Boas has been given until 4pm on November 15 to respond to the charges.