Noise reduction plays a major role in the drive train of motor vehicles operating at higher speeds. Long-wave deviations of gear systems related to manufacturing and assembly errors, such as tooth pitch deviation and geometric eccentricity, exhibit circumferential variations and have been demonstrated to be significant contributors to noise generation. However, a comprehensive and effective model that considers multiple long-wave deviations simultaneously has seldom been studied. To fill this gap, a new numerical model of spur gear systems with long-wave deviations is established, in which the coupling effects of both tooth pitch deviation and geometric eccentricity are taken into consideration. A time-varying mesh stiffness (TVMS) analytical model for spur gear pairs is established, which considers the relationship of errors between pitch deviation and eccentricity. The time-varying contact state of the gear pair under periodic long-wave deviations is also analyzed. A translation-torsion coupled dynamic model is established to investigate the excitation behavior of gear pairs with periodic long-wave deviations. The accuracy of the TVMS and the dynamic model is verified through comparisons with reference and experimental results. Results show that gear pairs with long-wave deviations exhibit periodic fluctuations in TVMS compared to ideal gear pairs, accompanied by phase differences. The mesh stiffness impact phenomenon becomes less pronounced for higher gear precision under lower-load conditions. Conversely, the periodic vibration characteristics induced by eccentricity become less prominent for the lower gear precision level. The excitation behavior of the gear pair with pitch deviation is masked by eccentricity at lower rotational orders, but it still dominates at higher rotational orders. This method can predict the dynamic characteristics of gear transmission systems with periodic long-wave deviations, providing theoretical guidance for reducing the vibration and noise levels.