Introduction: Studies have shown that higher response levels can be obtained when the bone conduction stimulation position is closer to the cochlea. However, the morphological characteristics of round window niche and posterior tympanum in congenital aural atresia (CAA) and stenosis (CAS) patients were different from the normal. These affected the position of the cochlea at the cranial base. It was still unknown whether the distances from the cranium of CAA and CAS patients to the cochlea were the same as those of normal patients or not. Objective: To measure distances from various points on the lateral surface of the cranium to the cochlea and the cranium thickness on these points among a CAA group, CAS group and normal control group, which may provide valuable information for the better position of bone conduction stimulation. Methods: CT images of CAA, CAS patients and these patients’ healthy sides were analyzed. Firstly, the Frankfurt horizontal plane (Pfrkt) was established. Secondly, a model of part of the cranium was three-dimensionally reconstructed. Then, the Pfrkt plane was rotated down 20, 30 and 40° according to the superior margin of the external auditory canal. At every angle, points 25, 30, 35 and 40 mm away from the superior margin of the external auditory canal were marked out on the surface of the model and recorded as P20A, P30A, P40A, P20B, etc. The spatial distances between the cranium and ipsilateral cochlea were defined as lengths of points on the surface of the model to the cochlea apex (CA), cochlear base (CB) and modiolus midpoint (MM), respectively, recorded as P20A/CA, P20A/CB, P20A/MM, P30A/CA, etc. Results and Conclusions: In all groups, the length of P20D/CA was the shortest compared to P30D/CA and P40D/CA (p < 0.05). The P20A/CB and P20A/MM were also the shortest (p < 0.05). When the Pfrkt plane was rotated down 30 and 40°, the results were the same as at 20° (p < 0.05). However, P20D, P30D and P40D were almost on the mastoid air cells. We suggest that the bone conduction stimulation position is placed closer to the ear, while avoiding the mastoid air cells in the CAA and CAS patients.