Purpose <p>Aircraft bay door drive system is characterized by long transmission chain and compact structure. Under the action of aerodynamic load, the system is prone to deformation and hysteresis, which prevents the bay door from opening and closing smoothly and accurately.</p> Methods <p>Considering the nonlinear factors such as time-varying meshing stiffness and backlash, a dynamic model of the aircraft bay door drive system is established. The correctness of the model is verified by comparing the response with motor control system model. The influence laws of different system stiffness on the natural characteristics are explored. Additionally, the frequency resonance analysis is carried out for the system speed excitation. On this basis, the degree of deformation of the bay door is defined, and the effects of different factors on the dynamic behavior of the bay door drive system are analyzed.</p> Results <p>The right and left elastic shafts exert a significant influence on the low-order natural frequency of the system. The system exhibits a considerable amount of mode jumping. Additionally, the system may experience resonance within the stable operating speed range, and the diameter of the drive shafts have a significant effect on the resonance speed. The backlash of the gear pair, time-varying meshing stiffness of gears and stiffness matching of the drive shafts all have a significant effect on the vibration of the system and the deformation of the bay door.</p> Conclusions <p>This study supplies some guidance to the design, speed adjustment and monitoring of bay door drive systems.</p>