The present invention relates to method and system for bite registration using multiple bite registrations. In this method or system, when both the 3D teeth model of the upper jaw and the 3D teeth model of the lower jaw are successfully aligned with the bite surface, the bite surface with the 3D teeth models of the upper jaw and the lower jaw is displayed for further evaluation; the bite surfaces selected by the user are combined to generate a final bite registration. Using multiple bite surfaces for registration improves the accuracy.