The lyrics of this song are a word-play : it's a kind of verbal joke based on an expression having two meanings. It's also unoriginal : there was a song released way back in 1979 which used the same word-play, entitled 'If I said you had a beautiful body, would you hold it against me?'.
If you 'hold something against someone' it can mean that you feel angry and resentful about something that they have done. So, you could say, 'If did this, would you hold it against me?', meaning 'Would you think badly of me if I did this?'
In a more literal sense, it can simply mean that you put something close to that person's body. The lyrics here mean both - it's a question about how the other person would feel if the singer said something, but it's also a flirtatious request for the other person to make physical contact. But the joke's been made before.