I'm trying to connect transformer to my ac unit but the confusion is the side for 220v comes with 3 wires, how can I connect the transformer?
1 it COM
The other 2 wires 208v- 240v, my unit is 220v and I'm trying to figure how to connect the power to this transformer.

How about providing the make and model number of the transformer so we can find the wiring diagram?

Use the 208-240 wires only. Make sure you do not have a two transformer system where the AC has a transformer and the heater has one, too. This is rare, though. It's easy to wire up the transformer, but it should have an in-line fuse or circuit breaker built in the transformer to protect it. You want to test the outside contacter to make sure the coil resistance is not too low, or you will burn out another transformer. A fuse or circuit breaker will protect the transformer.