Vegetation cover structure is a key factor affecting slope erosion process. Based on the simulated rainfall experiment carried out on a slope covered by natural vegetation in Luoyugou watershed of loess hilly region, the effects of three different cover structures on slope runoff and sediment yield were studied under the condition of 90 mm/h rainfall intensity. These three cover structures included the underground root system, the underground root system plus the surface crust, as well as the combination of underground root system, the surface crust and the vegetation canopy. The results were as follows:(1) The root system of the vegetation played a leading role in enhancing soil infiltration, the amount of soil infiltration and the steady infiltration rate on the vegetation root slope increased by 67% and 39.7%, respectively, compared with those on bare slope. (2) For the three vegetation cover structures, the surface crust had the best regulation effect on the runoff and sediment yield, and the contribution rate of runoff reduction and sand reduction was 43% and 67%, respectively. (3) There was a power function relationship between the accumulative runoff yield and accumulative sediment yield in the vegetation root plot and the bare plot, and the relationship turned out to be linear function with the superposition of vegetation cover structure. (4) The multi-level vegetation cover structure could prolong the development period and shorten the active period of the slope erosion process. The research results were important for quantitative evaluation of the effects of vegetation measures on water and sediment reduction.