Background The temporal bone has the most complicated anatomic feature among the whole human body, which always challenges otolaryngologists. This study was to study three-dimensional (3D) morphology of the temporal bone and the ear by means of a computer image processing technique, for the purpose of providing a 3D image to help in pathological, diagnostic and surgical procedures. Methods Forty sets of temporal bone celloidin serial sections with reference points were prepared and the contours of selected structures and reference points were entered into a graphics programme. The technique of computer-aided 3D reconstruction was applied to obtain 3D images and parameters of the temporal bones and the ears. Stereo views of the ossicles (n=5), the facial nerves (n=11), the posterior tympanic sinuses (n=11), the posterior ampullary nerves (n=4), the endolymphatic ducts and sacs (n=5), and the bony and membranous labyrinth (n=1) were reconstructed. Results Three-dimensional images, including the cochlea, the ossicles, the nerves, the tendons and the endolymphatic fluid system in the temporal bone, were obtained. Stereo picture pairs and 3D parameters of spatial dimensions, angle and volume for these reconstructed structures were calculated. The arrangement of the ossicles, spatial relationship of the bony and membranous labyrinth, the whole course of the facial nerves, the endolymphatic sac and posterior tympanic cavity were clearly observable. Stereo picture pairs made the spatial relationships among the above-mentioned structures much clearer. The operation of the posterior ampullary nerve transection was designed and simulated on the graphic computer based on 3D anatomic investigations. Conclusion The technique of computer-aided 3D reconstruction provides a new tool to observe the morphology of the temporal bone and thus may allow design and study of new surgical approaches.