Bevel gears are widely used in aerospace transmission systems as well as modern mechanical equipment. In order to meet the needs and development of aerospace, high-speed dynamic vehicles, and various defense special equipment, higher and higher requirements are made for the high precision and stability of gear transmission systems, as well as the prediction and control of noise and vibration. Considering the nonlinear factors such as comprehensive gear error and tooth side clearance, a dynamic model of the three-stage gear transmission system is established. The relevant physical parameters, geometric parameters, and load parameters in the gear system are considered random variables to obtain the stochastic vibration model. When the random part of the random parameters is much smaller than the deterministic part, the vibration differential equation is expanded into a first-order term at the mean of the random parameter vector according to the Taylor series expansion theorem, and the ordering equation is solved numerically. Based on the improved stochastic regression method, the nonlinear dynamic response analysis of the three-stage gear train is carried out. This results in a relatively stable system when the dimensionless excitation frequency is in the range of 0.716 to 0.86 and the magnitude of the dimensionless integral meshing error is < 1.089.