Conductive hearing loss is caused by a variety of defects, such as chronic otitis media, osteosclerosis, and malformation of the ossicles. In such cases, the defective bones of the middle ear are often surgically reconstructed using artificial ossicles to increase the hearing ability. However, in some cases, the surgical procedure does not result in increased hearing, especially in a difficult case, for example, when only the footplate of the stapes remains and all of the other bones are destroyed. Herein, the appropriate shapes of the reconstructed autologous ossicles, which are suitable for various types of middle-ear defects, can be determined by adopting an updating calculation based on a method that combines numerical prediction of the vibroacoustic transmission and optimization. In this study, the vibroacoustic transmission characteristics were calculated for bone models of the human middle ear by using the finite element method (FEM), after which Bayesian optimization (BO) was applied. The effect of the shape of artificial autologous ossicles on the acoustic transmission characteristics of the middle ear was investigated with the combined FEM and BO method. The results suggested that the volume of the artificial autologous ossicles especially has a great influence on the numerically obtained hearing levels.