When Pi is first introduced to the concept of Christianity in chapter 17 of the text, he is baffled by the central story of the religion:
What? Humanity sins but it's God's Son who pays the price? I tried to imagine Father saying to me, Piscine, a lion slipped into the llama pen today and killed two llamas...I have decided that the only way the lions can atone for their sins is if I feed you to them.
Yes, Father, that would be the right and logical thing to do. Give me a moment so that I can wash up.
So the comparison is between God's only son being sacrificed to forgive humanity for their sins and a zookeeper's son being sacrificed to allow the violent lions clearance for their sins.
To understand why Pi would make this connection, you must also remember that Pi discovers the story of Christ a few years after his father had taught him a vivid lesson about the instincts of lions (in chapter 9, Pi's father feeds a goat to a starving lion in front of his two sons so they can learn the instinctual violence of the animal and beware). Before the above quotation, Pi had wandered into the Christian church and seen the Cross with Jesus Christ hanging on it; he had remarked on the violent detail of the statue:
The victim [Christ] again, bruised and bleeding in bold colours. I stared at his knees. They were badly scraped. The pink skin was peeled back and looked like the petals of a flower, revealing kneecaps that were fire-engine red.
With a first impression of Christ showing a bloody and battered victim, it is no wonder that one of the first moments Pi thought of upon hearing the story of this Son was his father's graphic lesson to him a few years earlier.