The answer to this question is a most emphatic NO. God did not actually have sex with Mary to conceive Jesus. The Bible clearly says that “The Holy Spirit will come upon you, and the power of the Highest will overshadow you,” (Luke 1:35, NKJV). This is simply a ridiculous misunderstanding of the scripture. Mary was a willing bearer of the Christ Child, as she said to Gabriel on his announcement of the Lord’s intentions “Behold the maidservant of the Lord! Let it be to me according to your word,” (Luke 1:38, NKJV).
First and foremost, it is important to realize that these kinds of accusations and questions regarding scripture by skeptics may not be based in a real desire to find the truth, but a desire to simply BE skeptical. The best answer for atheists who make this claim is to simply point out their gross misconceptions about the nature of the conception and birth of Jesus Christ, namely that God had to physically force himself upon an unwilling participant. Instead, God, through the amazing power of the Holy Spirit, brought forth the immaculate conception of Christ through Mary, His willing servant.
This answer provided to the ministry of http://www.gotquestions.org.