Clarifying the impact of underlay (i.e., the combination of near-surface vegetation and surface micro-topography) on the surface runoff process would provide a significant theoretical basis for the adjustment of vegetation patterns and the control of soil erosion on steep slopes in mountainous areas of southwestern China. In the current study, the runoff process under different rainfall characteristics was observed based on 10 natural runoff plots, and the correlation between the spatial pattern of cypress (Cupressus funebris), micro-topography, and runoff characteristic parameters was tested using the Pearson correlation coefficient method. The coupling effects of the spatial pattern of cypress and micro-topography on surface runoff also were analyzed using the Response Surface Method (RSM). The results showed that (1) under the conditions of long-duration moderate rainfall or long-duration rainstorm, topographic relief, surface roughness, runoff path density, contagion index of cypress, and stand density of cypress were the main reasons for the difference in the peak flow of each runoff plot, while under the condition of the short-duration rainstorm, the factors previously mentioned were no longer the dominant factors; (2) under the conditions of long-duration heavy rainfall or long-duration rainstorm, the common laws reflected by the response of the peak flow to the composite index of the spatial pattern of cypress and micro-topography were that (1) when the composite index of the spatial pattern of cypress (V) was below 21 and the composite index of micro-topography (U) was below 10.5, the peak flow would not be significantly affected; (2) when U > 10.5, increasing the composite index of the spatial pattern of cypress within a certain range would promote peak flow; (3) when U < 7.5 and V > 18, the increase of V value could significantly reduce the peak flow, and on this basis, adjusting the V value to 41, the reduction rate of peak flow could reach 84%.