Based on the background that the Xin'an River Basin is a strategic water source and water conservation area for the integrated development of the Yangtze River Delta, studying the changes in the ecosystem service value of the Xin'an River Basin and the trade-off and synergy between ecosystem services are of great significance to promote the construction of the basin's ecological civilization system. At the same time, it also has an important enlightening effect on promoting the coordinated development of man-land relationship. Using the analysis methods of ecosystem service change index, correlation coefficient and spatial autocorrelation, the development and change of the ecosystem service value and the balance and synergy between ecosystem services in the Xin'an River Basin from 1999 to 2019 are quantitatively measured and analyzed. The results show that (1) the ecosystem service value of the Xin'an River Basin has fluctuated and declined as a whole. After the implementation of the ecological compensation mechanism, the overall ecosystem service value of the Xin'an River Basin has rebounded, and the improvement trend has gradually appeared. After the implementation of the pilot work of the ecological compensation mechanism, the ecological effects of land cover types represented by rivers and lakes in the protection and restoration of watershed ecosystems have been significantly strengthened, and the hydrological regulation service has the highest value among those ecosystem services. (2) The spatial distribution of ecosystem service value in the Xin'an River Basin is relatively stable overall, but the spatial difference and heterogeneity is quite strong, and there are obvious high-value agglomeration and low-value agglomeration areas, and the correlation is strong. The related types are mainly positive correlation. High-value areas of ecosystem services are concentrated in the Qiandao Lake and surrounding areas of Zhejiang Province, and the areas with relatively obvious gains in ecosystem services are mainly distributed in the upper reaches of the basin in Anhui Province. (3) The synergy relationship is the main body of the correlation relationship between the ecosystem services of the Xin'an River Basin, which mainly exists between the adjustment, support, and cultural service subsystems. After the implementation of the pilot ecological compensation mechanism, the correlation between hydrological regulation services and other ecosystem services has undergone a significant transformation. At the town level, the distribution of synergy between different ecosystem services is relatively consistent, and the correlation between various ecosystem services presents the characteristics of synergy relationship, and the balance relationship is mainly high and low agglomeration, which is most obvious between cultural service and support service.