"The word Messiah is a title and it's a title that has only been earned by one person and that one person is Jesus Christ," Judge Lu Ann Ballew said.
Ballew ordered Martin and Messiah's father to change their son's name to "Martin DeShawn McCullough," using both of their surnames.
Martin, whose two other children are named Micah and Mason, said she plans to appeal the decision.
"I was shocked. I never intended on naming my son Messiah because it means God and I didn't think a judge could make me change my baby's name because of her religious beliefs," she said.
"Everybody believes what they want so I think I should be able to name my child what I want to name him, not someone else," she said.
Ballew said that such a name would create problems for a child growing up in a Christian community.
"It could put him at odds with a lot of people and at this point he has had no choice in what his name is," Ballew said.
Despite the judge's objections, Messiah is the nation's fourth fastest-growing baby name.