"It is on its way" is a common expression that means "it's arriving soon."
The word "way" can mean "road" or "path," in English, like in the common question for directions: "Do you know the way to ______?" (the beach, main street, the hotel, etc.).
So the phrase "It's on its way" is a way of saying "it is on its path to you." It is very common to hear this expression when you are waiting for something: a delivery to your home or office, a meal at a restaurant, a letter or package, etc. You can ask "Is it on its way?" and the other person can reply, "Yes, it's on its way right now."
I hope this helps!