The water supply services of the Li River are essential for the ecological environment and local social development. Based on the InVEST model, we quantitatively analyzed the spatial and temporal distribution patterns of water supply services in the Li River Basin from 2000 to 2018 at multiple scales, including the raster, sub-basin, and regional scales, clarified the differences in water yield among different land use types, and explored the different stages of changes in the characteristics of water services. The results revealed four key aspects of this system. (1) The water supply service of Li River Basin showed a spatial distribution pattern of high in the north and low in the south, and the water yield gradually decreased from north to south. (2) Among the various land use types in Li River Basin, the average water supply capacity decreased in the following order: artificial surface, unused land, grassland, forest, cropland and wetland. (3) The average amounts of water services in the 18 sub-basins varied widely, with four sub-basins belonging to the high-value area for water supply services, eight in the middle-value area, and six in the low-value area. (4) From 2000 to 2010, the regions with large fluctuations in water supply services include the midstream region, Lipu River region, and the northern region of Gongcheng River; while from 2010 to 2018, the areas with large fluctuations were in the midstream region and Gongcheng River region. The results of this research increase our understanding of the water supply services in the Li River Basin and provide a critical scientific basis for the reverse compensation of a regional ecological compensation mechanism.