Under the control of the Loess Plateau, the northern part of the West Qinling Mountains has obvious transitional features in terms of topography, climate, soil and vegetation. In order to explore the effects of the Loess Plateau on habitat quality (HQ) of the West Qinling Mountains, we selected five typical counties with different percentages of the Loess Plateau area based on geomorphic types, climate, water system, vegetation zone, and elevation, and analyzed the spatial and temporal differentiation characteristics of HQ and their influence mechanisms with the help of the InVEST model and geographical detector (GD) model. The results showed that: (1) From 2000 to 2020, the three regions showed a decreasing trend of cultivated land and an increasing trend of forest as the area of the Loess Plateau within the region decreases. (2) From 2000 to 2020, HQ changes showed a bipolar sharpening phenomenon. (3) From 2000 to 2020, the mean HQ showed a trend of first increasing and then decreasing. HQ of the Loess Plateau, the Transition Zone, and the West Qinling Mountains showed a three-level gradient of low, medium, and high. the Transition Zone generally showed the spatial distribution characteristics of low in the north and high in the south, and the low grade were mainly distributed in the Loess Plateau area within the county north. The formation of this geographical distribution verified that the ecological effects of the Loess Plateau have influenced the HQ of the West Qinling Mountains. (4) Land use intensity and population density were the dominant factors causing spatial differentiation of HQ in the three regions, NDVI and NPP have always played a key role in the variation of HQ in the Transition Zone, and the synergistic enhancement effect between various factors promotes the change of regional HQ.