The Nativity was created by congregant and artist John Zachary, who has designed the church's Nativity for several years and usually uses the opportunity to address social issues, the Los Angeles Times reported Saturday.
Zachary said he decided during the summer that he would include Martin in the Nativity.
"He was, in my view, an innocent child like the innocent children killed by King Herod," Zachary, 57, said of Martin. "I think the Nativity has to be relevant to our time. I think Jesus is a symbol of hope and I think he has to be seen in today's context."
However, the scene has many people upset, calling the Nativity "sacrilege" and an "abomination."
"How sad to replace the Savior in the nativity scene," one person posted on Facebook. "What kind of church is this??? I pray that you will understand the real reason for the season..."
"No Christian I know would ever disparage Jesus Christ with such a repulsive image," wrote another. "I would never attend your church as a fellow Methodist and you ought to be ashamed of yourselves."
The Rev. Dan Lewis, a pastor at Claremont United Methodist Church, said he fears many people who saw and commented about the Nativity online only saw a picture of it and did not read Zachary's artist statement, which was posted on a placard right next to the scene.
"Nothing is done flippantly here," Lewis said. "It's got great thought, great depth and great meaning."