Abstract: This paper explores the spatio-temporal characteristics and influencing factors of habitat quality along the Yellow River in Shandong Province. It aims to furnish direct policy recommendations that are tailored towards enhancing ecological environmental protection and fostering high-quality socio-economic development at the county level. Using land use data in 2000, 2010 and 2020, the spatio-temporal distribution patterns and evolution characteristics of habitat quality were analysed by InVEST model. On this basis, the spatial autocorrelation model was employed to further explore the spatial differentiation of habitat quality, and subsequently the impact of social, economic, and natural factors on habitat quality were investigated by using the geographically weighted regression (GWR) model. The analysis reveals three results: (1) From 2000 to 2020, the average habitat quality index along the Yellow River in Shandong Province was 0.448, with a spatial distribution pattern where the middle and upper reaches exhibited lower quality, while the lower reaches showed higher quality. The habitat quality in the basin exhibited a decreasing trend with diminishing pace, particularly noting a pronounced downward trend in the middle reaches. (2) Spatially, habitat quality variation displays significant agglomeration, influenced by adjacent regions, and the overall agglomeration trend is consistently increasing. The area of HH-type agglomeration is notably larger than that of LL-type agglomeration, predominantly distributed in the lower reaches of the basin. (3) Land development intensity emerges as the primary factor influencing the spatio-temporal distribution of habitat quality. Population density, urbanization level, and NDVI also play important roles. The GWR model reveals that social, economic, and natural factors together contribute to significant spatial heterogeneity in the temporal and spatial variations of habitat quality. Identifying these spatiotemporal disparities is key to advancing high-quality ecological development in the area.