Habitat quality is an important indicator for measuring regional biodiversity and ecosystem service value. A change in habitat quality is the direct result of the interaction between human activities and the natural environment. In this study, the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model was used to evaluate the habitat quality of the Yellow River Basin (YRB) from 1980 to 2018. We further analyzed the quantity and spatial transfer status of habitat quality quantitatively using the Geo-informatic Tupu method. The results show that the habitat degradation degree under human disturbance showed a trend of increasing first and then decreasing, with values of 0.0196 in 1980, 0.0200 in 2000, and 0.0199 in 2018. In addition, it presents two ring structures: light-severe-high-moderate and light-moderate-high-severe in space. The overall level of habitat quality in the basin is relatively good, but there is a trend of decline, which are 0.6091, 0.6069, and 0.6049 in the three stages respectively. The spatial distribution of habitat quality showed a pattern of high in the middle and low on both sides. The habitat quality has been restored in some areas. The transition between good and medium and good and excellent in the Tupu change units of the habitat quality grade is the most intense. Both stages are mainly the transformation from high-grade to low-grade habitat quality, but there is a trend of gradual improvement. The findings could have theoretical support and policy implications for the maintenance of biodiversity and the protection of the natural environment in the Yellow River Basin.