The Daily Mail newspaper reported in February that Henry had said the club wanted to limit the number of African players in their squad because “they have a bad attitude” and “cause mayhem” when not in the team.
West Ham suspended and then sacked Henry on Feb.2.
The FA said in a statement that Henry had been charged with “misconduct in relation to comments he made which are alleged to be improper and/or insulting and/or abusive.”
It added that this was an “aggravated breach” of the rules because it included “reference to ethnic origin and/or race and/or nationality and/or colour.”
Henry has until May 15 to respond.
Reporting by Alan Baldwin, editing by Pritha Sarkar