Transmission error, to a certain extent, is one of the most important indexes to evaluate the meshing performance of spiral bevel gears, which directly reflects the transmission meshing characteristics of the Spiral Bevel Gears and is closely related to the shafting structure. This paper mainly studies the positive design calculation method between shaft structure and transmission error, and proposes a numerical calculation method of the spiral bevel gear transmission error considering the influence of shaft deformation based on the common software tool platform. It is compared with the international advanced design software (KIMoS software) of spiral bevel gear to verify the calculation method of the paper. The influence of shaft deformation on the transmission error of aero-engine spiral bevel gears is analyzed aiming at two kinds of design schemes for shaft structures in this paper. The analysis results show that the different forms of support have little effect on the contact force of the tooth surface, but the support form and the deformation of the shaft have a greater impact on the transmission error. Good transmission error curve of spiral bevel gears can be obtained by changing the support structure of the shafting system. Therefore, the work of this paper can provide reference for studying the relationship between shafting structure and transmission error of spiral bevel gear.