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.