Aiming to the puzzle that the inner load of nonlinear synthesis transmission system is difficult to obtain, a new kind of virtual prototype establishment and simulation method is put forward. The influence on nonlinear vibration with flexible rotor, bearing backlash is analyzed based on a virtual prototype. To validate the virtual prototype of nonlinear gear transmission system, the corresponding test platform is established. The consistency between simulation results and test results proves that the simulation results of the virtual prototype can be used to calculate the fatigue reliability life of key components. A new kind of fatigue reliability life prediction method of gear system considering multi-random parameter distribution is put forward based on the fatiguestatistic theory. Considering the periodicity of gear meshing, linear interpolation method is adopted to obtain the stress-time course of random load spectrum based on the gear’s complicated torque provided by virtual prototype. The gear’s P-Sa-Sm-N curved cluster can be simulated based on material’s P-S-N curve. The simulation process considers the parameter distributions of stress concentration coefficients, dimension coefficients and surface quality treatment coefficients, and settles the puzzle that traditional test methods cannot acquire the gear’s fatigue life of all reliability levels. This method can provide the distribution function and the interval of fatigue reliability life of gear’s danger region, and has a guide meaning for the gear maintenance periods determination and reliability evaluation.