Based on the InVEST model and integrating the use of the Geodetector and Geographically Weighted Regression (GWR) model, this paper dynamically analyzed the spatio-temporal evolution characteristics and driving mechanisms of habitat quality in Gannan Prefecture at the county scale from 2000 to 2020. The results show that: 1) From 2000 to 2020, habitat quality continuously deteriorated, with an average annual decline rate of 0.0016a^-1. The spatial distribution was relatively stable, showing a pattern of high in the southwest and low in the northwest-southeast. Hotspots were concentrated in Maqu County and Luqu County, while coldspots were distributed in a band or patch form around towns and in areas with dense road networks, mainly consisting of construction land and cultivated land. 2) The mutual conversion of land use types had a negative impact on habitat quality, with a cumulative decline of 0.031 in the habitat quality index. The conversion from forest land and cultivated land to grassland and from cultivated land to forest land were the main types that improved habitat quality. However, the conversion from ecological land to living and production land and from grassland to cultivated land was continuously expanding, with an average annual conversion area of 20.22 and 194.05km² respectively, further intensifying the risk of habitat degradation. 3) Elevation (0.459), average annual temperature (0.433), average annual precipitation (0.349), average annual evaporation (0.345), GDP (0.274), and population (0.269) were the main driving factors of habitat quality differentiation, and the interaction between these factors was nonlinearly enhanced or double-factor enhanced. The interaction between elevation and other factors was the strongest, with a contribution rate of over 45%, which had a decisive influence on the spatial distribution of habitat quality. 4) The impact of different factors on habitat quality in space was significantly different (P < 0.05). Average annual temperature, average annual evaporation, GDP, and population mainly had negative effects on habitat quality, while elevation and precipitation had significant positive effects. Below 3200m, habitat quality was relatively low, ranging from 0.045 to 0.203, with severe degradation fluctuating between 0.146 and 0.232. Above 3200m, precipitation was abundant and habitat quality was relatively high (0.383~0.759), but this area was more sensitive to climate change, with low grassland continuity and point-like habitat degradation. In future environmental protection, strict control over the expansion of construction land should be implemented, the system of land use control for cultivated land should be strictly enforced, and differentiated and diversified regulatory strategies should be adopted considering the characteristics of different driving factors. At the same time, attention should be paid to the impact of climate change on habitat quality in high-altitude areas, and through refined regulation of the human-land relationship and strategies to address climate change, the overall quality and efficiency of habitat should be improved.