Taking a high- speed motor train unit transmission gear system as an example,by using gear analysis software KISSsoft,the deformation of gear supporting axial in the transmission process is calculated.Through the method of modification to compensate the influence of the shaft deformation on the gear meshing performance. Then,the difference between before and after the modification of gear meshing contact spot,tooth surface line load distribution and the transmission error,etc are compared to ensure the motor train unit gear transmission system working more stable and reliable. The work of the research has important reference value to the design of the motor train unit gear pair.