@kowsar.ahmed it's possible there are pictures or videos that were sent as text or iMessages that could be taking up space. Also if you have email accounts setup they could be using a significant amount of space. Have a look at Settings -> General -> Storage & iCloud Usage -> Manage Storage (under the Storage section and not the iCloud section) to get a detailed listing of what is using up your storage.

It's also possible that the unused space on the phone was not properly marked as such. If you plug the phone into itunes, do you see most of that space taken up by "Other"? This is usually an indication of a corrupted iCloud backup that doesn't properly label the unused space, so the phone assumes there's something there despite it actually being empty.