Current research on the relationship between land use change and habitat quality and the driving factors, interactions, and future changes under multi-scenarios remains limited, especially in the ecologically fragile Yellow River Basin (YRB). Using the 2000, 2010, and 2020 land use data, we coupled FLUS with the InVEST model to analyze the relationship between land use change and habitat quality and predict habitat quality under 4 development scenarios. The driving factors were quantitatively identified by their interactive effects by utilizing Geodetector. The results showed that: (1) Overall, habitat quality of the YRB was moderate with an improving trend but exhibited significant spatial heterogeneity. The spatial distribution of habitat quality aligned closely with land use patterns. Habitat degradation showed a spatial pattern of “central-high, peripheral-low; eastern-high, westernlow”. (2) Land use was the primary driver of habitat quality differentiation (q > 0.8), with population density and GDP gaining influence. Factor interactions, especially between land use and other variables, exceeded individual effects. (3) Under the ecological space priority scenario, habitat quality improves significantly, especially in fragile zones where policy interventions are effective. Conversely, the production space priority scenario risks habitat degradation, necessitating measures to mitigate ecological pressure caused by industrial mining and urban expansion.