Objective This study aims to investigate the response status， regional differences， and influencing factors of habitat quality and landscape patterns in the Huaihe River basin and the Haihe River basin， providing theoretical support and a scientific basis for decision-making in the development of differentiated ecological protection strategies for the river basins. Methods Land use data from five periods between 2003 and 2023 were selected. The InVEST model was used to evaluate habitat quality in the river basins， and landscape pattern indices were calculated. The bivariate spatial autocorrelation method was employed to analyze the response relationship and inter-basin differences between the two. Furthermore， the explanatory power of physical geographical factors on the spatial differentiation of habitat quality was explored. Results 1） Cultivated land area decreased significantly in the Huaihe River basin （-20 394.68 km²） and the Haihe River basin （-13 783.16 km²）， while the areas of forest land， water bodies， and construction land all increased. Habitat quality was predominantly at low levels and declined over time， with decreases of 6.48% and 6.55%， respectively. 2） Habitat fragmentation gradually intensified in both river basins， while patch shape complexity remained stable （FRAC_MN fluctuation < 0.003）. Habitat quality in the Huaihe River basin showed a positive correlation with contagion （CONTAG） and prominent negative responses to patch shape complexity and land distribution uniformity. In contrast， habitat quality in the Haihe River basin was mainly negatively affected by the intensification of fragmentation. 3） Topographic factors were the core driving factors of habitat quality changes in the Huaihe River basin （q = 0.295） and the Haihe River basin （q = 0.467）， followed by atmospheric pollution stress （PM_2.5， O₃）， exhibiting spatiotemporal dynamics. The explanatory power of the interactions among natural environmental factors was stronger than that of single factors. Conclusion The evolution of habitat quality in the Huaihe River basin and the Haihe River basin exhibits differentiated characteristics. The heterogeneity of the response mechanisms between habitat quality and landscape patterns in the river basins requires the implementation of zonal governance and targeted restoration strategies to enhance the stability and service functions of regional ecosystems.