I didn't understand the usage. What does it mean and when can we use it?
It depends on the context, but the most common meaning is "having a significant effect on the moral status of an action". For example, "Is it morally important whether I kill someone or let them die?" This asks whether the moral status of an action can be different depending on whether it was active (killing someone) or passive (letting them die).
"Morally important" means important from a "moral" standpoint; having an important bearing on what's "right or wrong."