Bone mechanical function is given as a result of the material and structural parameters of bone tissue. We previously reported that the material parameter of regenerated bone can be evaluated dominantly using two indices of the density and the preferred orientation degree of biological apatite (BAp). In addition, bone morphology remarkably changes during bone regeneration, which may lead to a dynamic change in the mechanical function of whole bone. In this study, therefore, material and structural parameters of regenerated bone are analyzed separately. A 5-mm-long defect was introduced in rabbit ulna and spontaneously regenerated, and then a three-point bending test was conducted at the regenerated portion. The important parameter which dominantly controls the whole bone mechanical function shifts from a structural to material parameter during bone regeneration. Moreover, it was statistically demonstrated that the increase in the material parameter is strongly determined by recovery of the orientation degree of the BAp c-axis.