In this paper, we develop a caries investigation method based on fusion modeling of the external surface texture obtained by an intraoral scanner (IOS) with the internal images collected by cone beam computed tomography (CBCT). Mandibular permanent molars with occlusal caries are investigated in this study. Digital polygon file format files with colored textures generated by an intraoral scanner (IOS) and high precision CBCT images are collected on the same teeth. A new dental 3D model data format is proposed through data fusion and accurate registration compatible with external surface models and internal CBCT point clouds. The experimental results show that IOS-CBCT fusion image shows the structural information of caries more clearly and accurately than a single IOS or CBCT. After the steps of registration, fusion, and 3D reconstruction, the structure boundaries are clear and without overlap. The image fusion based on multimodal IOS-CBCT images lead to a great improvement in the fused image quality. The method is non-invasive, straightforward, and sensitive and can be very helpful in indicating exact conditions of dental caries, as well as non-caries dental hard tissue diseases, and pulp and periapical lesions.