As an important recharge source of dry season runoff, baseflow plays an important role in maintaining the basic flow of rivers and the health of the basin ecosystems. However, under the influence of ecological projects such as the Grain for Green Project and climate change, baseflow changes and their influencing factors have not been thoroughly analyzed. A comprehensive understanding of these dynamics is essential for effective water resource management and the sustainability of these ecosystems. Taking the Chao River watershed as the study subject, this study provided a comprehensive comparative analysis of the applicability of nine different baseflow separation methods based on the hydrological and meteorological data from 1961 to 2020. In addition, the Mann-Kendall trend test and the BFAST (Break For Additive Season and Trend) algorithm were employed to elucidate the time-varying characteristics of baseflow and the baseflow index (BFI). Furthermore, the dominant factors of the watershed's baseflow changes were determined through multiple linear regression and the slope change ratio of cumulative quantity methods. The study found that: (1) The two-parameter Eckhardt recursive digital filter method demonstrated relatively higher estimation accuracy, and the baseflow process line obtained using this method was more consistent with the actual changing characteristics of the Chao River's baseflow. (2) The annual baseflow showed a significant downward trend at a rate of ?0.22 mm/a, while the normalized difference vegetation index (NDVI) and BFI exhibited a significant increasing trend (P<0.001). Meanwhile, there were abrupt changes in both baseflow and NDVI in the year 1999. (3) Vegetation restoration emerger as the dominant factor contributing to the reduction of baseflow, with a substantial contribution rate range from 73.13% to 86.87%, followed by potential evapotranspiration (contribution rate of 13.13%—43.27%). Additionally, the increase in precipitation had a certain promoting effect on baseflow, with a contribution rate of 2.63%—16.42%. This study provided an important scientific foundation for the sustainable utilization of water resources and sustainable vegetation restoration in the Chao River watershed.