How did John the Baptist escape the murder of the Holy Innocents?
Scripture does not say. However, we might speculate that the reason was because Herod apparently limited the murder to the region (Matt. 2:16) where he knew the Messiah was to be born (Matt. 2:1-6). So far as we know, St. John the Baptist and his parents did not live in Bethlehem or its neighboring region — otherwise Mary and Joseph could have stayed with them when searching for a place to stay while in the area for the enrollment (Luke 2:4-7) — but in the hill country, in an unnamed city of Judah (Luke 1:39-40), which may have been distant enough from the attack directed by Herod to protect the infant St. John the Baptist.
