The Blues accuse the 37-year-old, who showed the side two red cards during Sunday's defeat to Manchester United, of "inappropriate language" towards a pair of 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."
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 striker received a second yellow card for what the official interpreted as a dive under the challenge of Jonny Evans.
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