To mitigate potential risks such as starter motor failures and control link malfunctions in the startup control system of emergency backup diesel generators in data centers—risks that may impede the generator’s normal startup—this paper proposes a dual-redundant starter motor cross-controller. The controller is designed to enhance the system’s fault-tolerance capability and ensure cross-control stability during the startup process. First, based on the PWM (Pulse Width Modulation) input characteristics of dual-redundancy motors, a cross-control strategy is constructed. Second, a dual-redundancy starting motor model is built according to the starting motor type, and fuzzy adaptive PID (Proportional-Integral-Derivative) is used to adjust the motor’s output speed. Subsequently, hardware PCB (Printed Circuit Board) and software logic are designed, followed by experimental verification. Results show: under fuzzy PID control, the diesel generator speed (0 to 1500 r/min) has a control accuracy error of 1.33%; under the dual-redundancy strategy, the standby motor switching response time is ≤ 0.3 seconds with 100% fault recovery success; traditional PID has obvious oscillation and overshoot in the initial 0.02 seconds, while fuzzy PID takes only 0.017 seconds to reach a stable state in motor simulation. This controller significantly improves key performance of dual-redundancy motors, such as starting reliability and control accuracy.