In this paper, the vibration characteristics of the helical cylindrical gear split-torque transmission system with diaphragm coupling misalignment are studied. Firstly, the 14-DOF nonlinear simulation model of the helical cylindrical gear split-torque transmission system are established. To improve the model accuracy, time-varying mesh stiffness, random backlash, mesh error and bending deformation of shaft are considered respectively. Secondly, according to the nonlinear simulation model, the differential equations are established, and the differential equations are sovled with the time-varying stiffness of diaphragm coupling misalignment. Finally, the relationship between the phase of bolt group in diaphragm coupling and the asymmetric property of the split-torque transmission system is determined by numerical methods. The results show that the asymmetric property of split-torque transmission system could be effectively improved by changing the phase of bolt group in diaphragm coupling. The method is proven effectiveness by a modification work involved in this paper, and have reference significance for solving engineering problems.