With the advent of large-scale development, extreme imbalance in the ecology of the Heihe River Basin (HRB) has caused a series of ecological problems. In order to explore the spatiotemporal variation of ecosystem services (ESs) and to assess the characteristics of ESs under the terrain gradient effect (TGE), the three key ESs were quantified based on the InVEST model using five series of land-use data obtained from remote sensing images from 2000 to 2020 in this study. The terrain index was used to analyze the influence of terrain on ESs. The results show that most of the ESs were in high numbers in the south and low numbers in the north, as well as high numbers in the middle and upper reaches and low numbers at downstream locations. It was found that high-quality habitats degrade to general-quality habitats, and poor-quality habitats evolve into general-quality habitats. It was also found that the water production volume continues to decline and soil conservation becomes relatively stable with little change. This study illustrates different ESs showing obvious TGE with changes in elevation and slope. These results indicate that the effect of land-use change is remarkable and TGE is highly important to ESs in inland watersheds. This research study can provide a scientific basis for the optimization of regional ecosystem patterns. The results are of great significance in terms of rational planning land use, constructing ecological civilizations, and maintaining the physical conditions of land cover at inland river basins.