An intraoral scanning system includes a motion sensing unit, an image sensing unit, a storage unit and a processing unit. The processing unit classifies first position information and second position information obtained by the motion sensing unit and the image sensing unit in an initial scanning process into first groups and second groups, wherein the first position information and the second position information are stored in the storage unit. The processing unit selectively uses the first groups or the second groups to perform comparison in a re-scanning process, so as to position an incomplete area in a model.