The FA alleges the relegated Seasiders failed to ensure spectators from entering the field of play while the match at Bloomfield Road was being played.
The game on the final day of the season was called off in the 48th minute after Blackpool fans staged a protest against owner Karl Oyston in the centre circle.
Referee Mick Russell was forced to take the players off the pitch with the score at 0-0 and, after the game was held up for more than an hour, the decision was taken to call it off.
This FA charge is separate to the Football League charge last week.
An FA statement said: “Blackpool have been charged by the FA in relation to crowd incidents during the second half of their match against Huddersfield Town at Bloomfield Road on 2 May 2015.
“It is alleged the club failed to ensure that no spectators or unauthorised persons were permitted to encroach onto the pitch area whilst attending this fixture, resulting in its abandonment.
“Blackpool have until 28 May 2015 to respond to the charge.”
The Football League charged the Tangerines for failing to fulfill their fixture against Town on the final day of the season, though the 0-0 scoreline was allowed to officially stand.