Introduction Understanding the spatiotemporal dynamics and drivers of habitat quality in the Huangshui River Basin is crucial for ecological conservation and restoration efforts in the cold and arid regions of the Qinghai-Tibet Plateau.Methods Utilizing land-use change data spanning from 2000 to 2020, we integrated the PLUS-InVEST model with the Geodetector method to quantify the trajectories of habitat quality and identify the key driving factors under four distinct scenarios: The Natural Development Scenario (NDS), Economic Development Scenario (EDS), Cultivated land Protection Scenario (CPS), and Ecological Protection Scenario (EPS).Results Our findings reveal the following: (1) Grassland remained the predominant land-use type from 2000 to 2020, with an average habitat quality index of 0.65. While overall habitat quality remained relatively high, a slight decline was observed, exhibiting a spatial gradient with lower values in the central basin and higher values toward the periphery. (2) By 2035, both NDS and EDS are projected to result in significant habitat fragmentation, primarily driven by the expansion of construction land, while CPS and EPS are expected to enhance habitat quality through the preservation of cultivated and ecological lands. (3) Land-use type emerged as the most influential factor driving spatial heterogeneity in habitat quality, with the interaction between land-use and temperature demonstrating the highest explanatory power.Discussion These results provide robust projections of future land-use patterns and their impacts on habitat quality in the Huangshui River Basin, offering a scientific foundation for sustainable basin management and ecological protection.