The Cornish Football Association has given Martin and his club two weeks to respond to the charge.
Martin was sent off after reacting angrily to a late penalty being awarded against his side in Tuesday's game with Tavistock, which they lost 4-1.
Following the red card, he allegedly assaulted referee Stuart Kane.
The Cornish FA has banned the former Exeter City and Truro player from all football-related activity while their investigation continues into a possible breach of FA rule E3, which covers physical contact, violent conduct and threatening and/or abusive language or behaviour against a match official.
Martin had already been suspended by his club over the incident in the South West Peninsula League Premier Division fixture.
"It's extremely disappointing that these allegations have had to come to us," said Cornwall FA governance manager Richard Pallot.
"It's one of our more high-profile clubs in the county, we will deal with it very quickly and we take these allegations very seriously.
"I have spoken to Stuart this morning. He's absolutely fine. he's obviously a little bit shaken up through the incident, but he's not in too bad shape," he added to BBC Radio Cornwall.
St Austell chairman James Hutchings said in a statement: "The club would also like to apologise publicly to all in attendance at the game, the FA, the SWPL and also to the referee Stuart Kane, who is a well respected match official throughout Cornwall and Devon,"
Martin played for Exeter City in 2004-05, including their FA Cup third-round draw at Manchester United and home replay defeat.
AFC St Austell midfielder Marcus Martin has been charged with improper conduct after allegedly attacking a referee during a game in Cornwall.