In this paper, a conjugate modification method for coaxial split-torque drive system considering structural deformation is proposed. First, a finite element model of the face gear coaxial split-torque drive system was established and the main deformations affecting the system's contact pattern were analyzed. Then, the compensation of deformation of the gear pair was obtained by changing the feed direction in the tangential and tooth depth directions of the grinding wheel during the grinding process, and the equation of the tooth surface after changing the feed path of the grinding wheel was derived. Furthermore, the effectiveness of this method is demonstrated by an numerical example. The results show that the modification method can reasonably compensate for the gear deformation, and the contact pattern coverage exceeded 80% along the face width direction; compared with the previous modification methods, the contact condition of the gear pair has been significantly improved. Finally, experiment of the face gear grinding was conducted, which validated the feasibility of the proposed method.