We have a 1.5yr old new roof. When the temperature is cold, in the winter, it makes cracking sounds in different areas, as if someone throws a rock at it. What causes that ? Will it always be like that ? The old roof never produced any such sounds.

Were there any repairs to the roof structure such as plywood or other sheathing replaced?
Also, depending on where you are located as the temperatures this winter may have been much lower than you have experienced since you have lived in the present house.
Also, snow load may be more than normal this year.
It is most likely contraction and expansion of materials but if you are still concerned, have your roof inspected by a reliable builder or roofer.