Understanding the effect of land surface characteristics on rainfall-runoff generation is crucial in mastering the mechanisms of soil and water conservation. To characterize rainfall-runoff generation in desert steppes and to quantify the contribution of different influencing factors, a field-simulated experiment with three land degradation levels and three rainfall intensities (RIs) was conducted in the Inner Mongolia Desert Steppe. The results revealed that rainfall-runoff generation in different degraded plots at various RIs differed significantly. The runoff was generated faster and accumulated larger volumes under high RIs and heavy degradation levels (HDs) in comparison with generation under moderate/light degradation levels (MDs/LDs) and moderate/low RIs. The accumulated runoff over 40 min under a high RI on the HD plot is 153.37 L, which is much larger (0.77 L) than that under a low RI on the LD plot. The result from the structural equation model (SEM) indicated that RI is the most important factor directly driving rainfall-runoff generation, and its standardized path coefficient reached a value of 0.52. The vegetation condition is the second direct factor, with a standardized path coefficient of −0.51. However, the soil water content (SWC) has an indirect impact on rainfall-runoff generation through affecting vegetation conditions. So, interactions also exist between variables such as vegetation and soil. Therefore, the rainfall-runoff generation in the desert steppe may be mitigated through an enhancement of the vegetation and soil properties or through optimizing the interaction relationship between soil and vegetation.