Skull identification is an important subject for research in forensic medicine. Current research can be divided into two categories: 1) craniofacial superimposition and 2) craniofacial reconstruction. Both categories rely essentially on the accurate extraction and representation of the intrinsic relationship between the skull and face in terms of the morphology, which still remain unsolved. They have high uncertainty and a low identification capability. This paper proposes a novel skull identification method that matches an unknown skull with enrolled 3D faces, in which the mapping between the skull and face is obtained using canonical correlation analysis. Unlike existing techniques, this method needs no accurate relationship between the skull and face, and measures only the correlation between them. In order to measure the correlation more reliably and improve the identification capability of the correlation analysis model, a region fusion strategy is adopted. Experimental results validate the proposed method, and show that the region-based method can significantly boost the matching accuracy. The correct identification rate reaches 94% when using a CT data set. This paper can provide a theory support for research on craniofacial superimposition and craniofacial reconstruction.