The continuous deterioration of terrestrial ecosystems has led to the destruction of many biological habitats in recent years. The Tumen River cross-border basin, an important biological habitat, is also affected by this changing situation. Assessing habitat quality (HQ) is crucial for restoring and protecting habitats, and vegetation plays a significant role in this process. In this study, we used geographical detector (GD) to extract fraction vegetation coverage (FVC) features and quantify the contribution of driving factors. By coupling vegetation cover and land use data, we assessed HQ. Our findings reveal a declining trend in FVC from 2000 to 2020, which mainly assumed a spatial pattern inclined from northeast and southwest to southeast. Human activities and natural factors interacted to cause these changes in FVC, with human activities having a more significant impact. Vegetation and land use changes led to a decline in the basin’s HQ index. This study highlights the crucial role of FVC in HQ and provides a relevant scientific reference for optimizing the evaluation of HQ in the Tumen River cross-border basin and promoting the sustainable development of regional ecology.