Mourinho, who is appealing against a Â£50,000 fine and suspended one-match stadium ban for comments made about officials following the October 3 loss to Southampton, faces further charges after being sent to the stands by referee Jonathan Moss during the ill-tempered derby at Upton Park.
A statement from the FA read: "Jose Mourinho has been charged with misconduct in relation to his language and/or behaviour towards the match officials in or around the dressing room area at half-time."
Silvino Louro, one of Mourinho's assistants, was sent to the stands after Nemanja Matic was sent off for two bookable offences and has also been charged with misconduct
Both the Hammers and the Blues have also been charged for failing to control their players in the aftermath of the challenge which led to Matic's dismissal.
"Chelsea coach Silvino Louro has also been charged with misconduct in relation to his behaviour which led to his 45th minute dismissal from the technical area," the FA statement added.
"West Ham have been charged for failing to control their players in the 44th minute of the game and Chelsea have also been charged with the same offence for an alleged breach in the 45th minute of the game.
"All parties have until 6pm on Thursday (October 29, 2015) to reply."
Source : PA