Huth appeared to respond to a Twitter account which posts sexual images of individuals and asks users to guess their gender.
The 30-year-old German has until 6pm on January 21 to respond to the charge.
The FA said in a statement: "It is alleged the comments were indecent and/or improper and/or brought the game into disrepute, contrary to FA rule E3(1).
"It is further alleged that this breach of Rule E3(1) is an "aggravated breach" as defined in rule E3(2), as it included a reference to gender and/or gender reassignment."
Huth apologised earlier in January for interactions he made after participating with a Twitter account which invited users of the social media site to guess from cropped photographs of people in explicit poses whether those pictured have male or female genitalia.
A series of tweets posted from Huth's official account showed the former Chelsea and Middlesbrough player taking part and making indecent remarks.
He deleted the tweets and posted a message saying: "Clearly no offence was meant or directed to anyone, but apologies if I've offended anyone."
In October the FA handed Rio Ferdinand a three-match suspension, as well as a Â£25,000 fine, for comments he made on Twitter, though that was not the QPR defender's first offence on social media.
Source : PA