The Blues accuse the 37-year-old, who showed their side two red cards during Sunday's defeat to Manchester United, of "inappropriate language" towards a pair of their players
The Blues are accusing the 37-year-old of using "inappropriate language" towards two of their players.
"We have lodged a complaint to the Premier League match delegate with regards to inappropriate language used by the referee and directed at two of our players in two separate incidents in today's match," a club spokesman announced after the game.
"The match delegate will pass the complaint to the Football Association.
"We will make no further comment at this time."
The Professional Game Match Officials Board, governing body for referees, said in a statement that it is "aware of the allegations and they are being treated with the utmost seriousness.
"Mark will cooperate fully and welcomes the opportunity for the facts to be established. No further comment will be made until the matter has been properly investigated."
Clattenburg sent off two Chelsea players, Branislav Ivanovic and Fernando Torres, during the match at Stamford Bridge, with home manager Roberto Di Matteo laying the blame for their loss at his feet.
The Serbian defender was dismissed for a professional foul on Ashley Young before the £50 million striker received a second yellow card for what the official interpreted as a dive under the challenge of Jonny Evans.