The source uncertainty causes spatial variability of ground motions in mountain-valley sites near the fault. This study aims to analyze how the uncertainty propagation in the source model affects the near-fault and local site effect when there is a mountain-valley site in the near-fault area. This study considers the uncertainty of the asperity intensity and rupture velocity by random variables, and considers the randomness of the position of the asperity and the initial rupture point by setting three rupture scenarios. The impact of the local site on the variability of ground motions is compared, and the correlation between the variability of ground motion and the fault distance and dip angle is discussed. To solve multi-dimensional uncertainty problems, the multiplicative dimensional reduction method (M-DRM) with high accuracy and efficiency is employed, and the physical process of fault rupture to site response is simulated by the indirect boundary element method (IBEM). The results indicate that M-DRM is applicable to solving ground motions in near-fault complex sites with uncertain parameters. The uncertainty is transmitted with the propagation of seismic waves, and the scattering of seismic waves in mountain-valley sites amplifies this uncertainty. The local site effect increases the frequency band ranges and peak values of velocity pulses, and the uncertainty only affects the values of the velocity pulses. Considering the mean plus once the variance caused by the uncertainty, the maximum value of vertical velocity pulse can be increased by 34%. The variability of ground motion parameters decreases with the increase of fault distance and dip angle. It is necessary to quantify the uncertainty of the sources in ground motion simulation based on physical models.