The habitat quality (HQ) of the Yellow River Basin (YRB) has undergone significant changes driven by rapid urbanization and population growth. Using the InVEST model, we assessed year-to-year changes in HQ over the period 1990-2020, analyzing spatial and temporal variability, key influencing factors, and potential responses under different land management objectives. Results showed that HQ in the YRB exhibited an overall increasing trend (0.76 per decade), largely attributed to afforestation practices. However, annual fluctuations emphasized the necessity of year-by-year analysis. Vegetation and elevation were identified as the main contributors to high HQ, highlighting the effectiveness of afforestation on steep slopes and around rivers/lakes in further improving HQ. Notably, the latter part of the upper Yellow River was identified as an ecologically vulnerable area with low HQ scores, suggesting the need to prioritize ecological restoration efforts in this region. These findings provide valuable insights for ecological management and advancing ecosystem service science.