The water line make a water hammer sound when toilet is flushed. Any ideas how to fix this. Recently replace guts of toilet if that helps?

Try to close the angle valve under the toilet tank 1/2 way and try if that will help, also tell us what type of fill valve do you have see the images below, Thanks.

John

I would start by shutting down the house main supply and then open the connection at the stop under the toilet. Allow the line to drain into a bowl, this will replenish the air supply to the likely built in hammer arrestor found in most homes. More specifically what I want you to do is disconnect the small line going up from the stop valve to the toilet, disconnect at the valve. Then open the valve to drain the water laying in the supply line