The Eagles lost 1-0 to Tottenham in their Premier League opener courtesy of a penalty, leading to the 50-year-old criticising the role of the officials
The FA have given the 50-year-old until August 23 to respond to charges which amount to improper conduct around the match officials changing room, as well as his post-match comments that were deemed to have brought the game into disrepute.
Holloway was incensed by referee Mark Clattenburg after the official waved play on after a possible foul by Nacer Chadli, before awarding Spurs a penalty for handball in the second half.
Speaking to reporters, Holloway said: "I've got to learn what a foul is because I thought Nacer Chadli deliberately body checked Stephen Dobbie, smashed him down and ran off with the ball.
"If the referee didn't see that, the assistant should have. You have to ask if he's good enough if he didn't see that. I don't see how he can miss it.
"It's going to be a long hard season for me with these people [referees]. I had this with Blackpool.
"Certain clubs get fouls and others don't. Tottenham will feel that if they play Man United.
"Do I think I would have got that at Tottenham? No I don't. I just want a bit of fairness."