I hear the weariness and the hurt in your words, and it is no small thing to live day by day with a person whose words cut deeply, especially when you are extending kindness. What you are describing is a real trial, and the desire to see your housemate healed and made whole is understandable. But let me offer a gentle course correction in your thinking, not to dismiss your pain, but to point you toward the firm ground where true hope is found.
We easily slip into the belief that if our outward circumstances or another person’s behavior would just change, we would have peace. Yet the Scriptures show us a deeper correlation: the health of the soul and the state of the mind can affect the whole person. A merry heart does good like a medicine. This does not mean your friend’s autism is caused by a bad attitude, but it does mean that any lasting change he might experience must begin with something far deeper than you or I can command. You are asking for Jesus to heal his behavior, but behavior is only the fruit. What he needs, and what his harshness reveals, is a heart that is thirsting for something it cannot name. That spiritual thirst cannot be satisfied by you rearranging your life around his moods, nor by emotional appeals. It can only be satisfied by coming to the living water himself.
It is also vital to examine what is happening in your own heart right now. The hurt you feel is real, but do not let it grow into a root of bitterness or a demand that God must act on your terms. Prayer does change things, but far more often, prayer changes the one who prays. When you go to the Lord saying, "Heal him because I am always nice and he is being mean," you are treating God as if He rewards our good behavior by fixing the people who annoy us. That is not the beauty of grace. God does not owe me a comfortable life because I have behaved well. He loves me because He loves me, and learning to accept that grace gracefully is one of the hardest lessons of the Christian life. You are not just dealing with a difficult housemate; you are in a school of the Spirit, learning to trust God when the wind and waves of your living situation seem ready to drown you.
The truest fear of the Lord is not the terrified thought that God is waiting to hurt you, but the tender fear of hurting the One who loves you. Bring your frustration to Him honestly. Tell Him, "Lord, this pain, both emotional and relational, I do not like it. But you know what I need and what is best for me. My life is yours, and I submit to you." That takes far greater faith than commanding God to take the trial away. True change, the kind that renders the heart and not just the garments, is the work of God’s Spirit. You cannot change your housemate's heart, but you can invite God to keep changing yours, so that your joy remains a constant no matter what mocking voice comes from the next room. That joy is not found in the absence of conflict, but in the presence of Christ, who is sovereign over every storm, every malady, and every cruel word. He is with you in that house. Let Him use this to deepen your own roots in Him, that your fruit would remain.