The dual-input single-output (DI-SO) cylindrical spur gear system possesses advantages such as high load-carrying capacity, precise transmission, and low energy loss. It is increasingly becoming a core component of power transmission systems in maritime vessels, aerospace, marine engineering, and construction machinery. In practical operation, the stability of the DI-SO cylindrical spur gear system is influenced by complex excitations. These excitations lead to nonlinear vibration, meshing instability, and noise, which affect the performance and reliability of the entire equipment. Hence, the dynamic performance of the DI-SO cylindrical spur gear system is thoroughly investigated in this research. The impact of excitations and nonlinear factors on the dynamic characteristics was investigated comprehensively. A comparative analysis of the gear system was conducted by establishing a bending–torsional coupling vibration analysis model under synchronous and asynchronous meshing conditions. Nonlinear factors such as periodic time-varying meshing stiffness, meshing damping, friction coefficient, friction arms, load sharing ratio, comprehensive transmission error, and backlash were considered in the proposed model. Then, the effect laws of excitations and nonlinear factors such as meshing frequency, driving load fluctuation, backlash, and comprehensive transmission error were analyzed. The results indicate that the dynamic characteristics exhibited staged stable and unstable states under different meshing frequencies and meshing conditions. At the medium-frequency meshing stage (0.96 × 104~1.78 × 104 Hz), alternating phenomena of multi-periodic, quasi-periodic, and chaotic motion states were observed. Moreover, the root mean square value (RMS) of the dynamic transmission error (DTE) in the asynchronized gear system was generally higher than that in the synchronized gear system. It was found that selecting the appropriate meshing condition could effectively reduce the amplitude of the DTE. Additionally, the dynamic performance could be significantly improved by adjusting control parameters such as driving load fluctuation (0~179 N), backlash (0.8 × 10−4~0.9 × 10−4 m), and comprehensive transmission error (7.9 × 10−4~9.4 × 10−4 m). The research results provide a theoretical guidance for the design and optimization of the DI-SO cylindrical spur gear system.