This paper presents an analytical model for gear-bearing systems to investigate the cage behavior in gear transmission systems and the influence of defective gear pairs on cage response. In this model, the dynamic models of spur gear pairs and cylindrical roller bearings are integrated. Subsequently, a mathematical framework for describing the spalling failure on the tooth surface is devised and added to the system equations. Based on the distinctive operating characteristics of the bearing cage, typical operating conditions for the system are selected. The findings demonstrate that when the bearing operates at low speed, the displacement oscillation of the rollers will be inevitably caused by bearing instability, which can be effectively suppressed by increasing the system speed. Periodic shock and pulse forces can be observed when localized failures occur on the gear tooth surface. The pulse force is transmitted to the support bearing through the shaft, disrupting the contact process between the cage and other bearing components. As a result, the driving force of cage translational motion is weakened, while the interference effect of rollers on cage motion is enhanced. The operational stability of the bearing cage is reduced, especially when the degree of failure is aggravated. However, the contact torque between the guide ring and cage is increased by the vicious shock, whereas the contact torque between the cage and rollers is weakened. The cage speed is slightly increased, and the slippage rate is reduced. Finally, the developed model is confirmed through experimental tests and the finite element method.