Michael Strahan is going to war with one of his ex-wives over custody of their twin girls ... and he claims his ex is abusing their kids.
Michael claims his second ex-wife, Jean Muggli Strahan, is physically and emotionally abusing their teenage daughters, Sophia and Isabella, and the ex-NFL star is gunning for a judge to strip Jean of primary custody and give it to him ... according to new legal docs obtained by TMZ.

Michael claims Jean's been engaging in a "pattern of abusive conduct towards the children for years" .