To study the nonlinear dynamic characteristics of the electric drive transmission system of clean propulsion vehicles, a rotor-bearing system consisting of dual-stage meshing gear pairs and multiple loaded bearings was established. The influence of time-varying meshing stiffness, tooth side clearance, bearing clearance, and other factors were considered. A multi-degree of freedom vibration differential of the system was established equation, to analyze the vibration characteristics of various parts of the transmission system under different parameters. Using time-domain diagrams, poincaré cross-sections, bifurcation diagrams, and other images to study the vibration of gears. In addition, the primary resonance stability equation of the system is derived and its stability under different conditions is analyzed using meshing damping, stiffness, and load as variables. The results show that as the rotational speed increases, the first stage gear of the system undergoes the “single cycle-bifurcation-chaos-bifurcation-single cycle” vibration process, while the second stage gear undergoes two such processes. The instability intervals can be obtained as [3092,4859] and [8098,10896] r/min, [2797,3533] and [9423,14135] r/min respectively. Avoiding these speed ranges helps to improve the stability and safety of automotive motion.