Abstract: The natural vegetation in the lower reaches in the inland basins of northwest China is strongly dependent on the groundwater ecological function, and the lithology and structure of the vadose zone has a significant impact on the groundwater ecological function. However, there is a lack of systematic and specific research on how to quantitatively analyze and evaluate the degree of influence. The natural oasis area in the lower reaches of the Shiyang River Basin in Gansu Province is taken as the research area, and field investigation, soil column test and numerical simulation with Hydrus1-D are carried out to study the ecological effect of the coupling effect between the vadose zone and groundwater. The difference of water supply ability and water holding ability of the vadose zone with different lithologic structure is analyzed, and the influences of lithology and structure of the vadose zone on the groundwater ecological function is quantitatively compared. The results show that (1) the lithological structure of different vadose zones has different effects on the groundwater ecological function when the groundwater depth increases or decreases. (2) When the groundwater depth decreases gradually, under the same vegetation condition, the finer the lithologic particles in the vadose zone, the higher the height and speed of the supporting capillary water rises, and the faster the soil obtains groundwater recharge, and the more beneficial it is to the growth of the surface vegetation. (3) The effective water holding capacity of the vadose zone in the arid area has ecological effect of maintaining the survival of land surface vegetation after the local groundwater depth increases greatly. The effective water holding capacity of the medium lithologic particles is the largest, which has the most obvious ecological effect on maintaining vegetation. Compared with a single lithology, the combination of multiple lithologies is more conducive to hold larger effective water capacity and stronger ecological effect. The results will be helpful to strengthen the understanding of the regulation of the vadose zone in groundwater ecological function, and can provide a scientific basis for the fine management of water resources and ecological protection in arid regions.