A reasonable ecological compensation scheme for watersheds is beneficial for water resource protection and ecological sustainability. The existing literature has few watershed ecological compensation (WEC) schemes based on long-term observation and large spatial scale analysis of ecosystem service value (ESV) and considering its realization in spatial planning. Therefore, in order to establish a WEC scheme and integrate it into spatial planning, we take the Middle Route of South-to-North Water Diversion Project (MRSNWDP), a water resource area protecting the water resources at a huge local economic development cost, as a case study, and calculate the change trend and change range of the watershed’s total ESV from 1990 to 2015, thus, forming the WEC scheme. The results show the total ESV in the study area shows a slight downward fluctuation trend from 1990 to 2015, decreasing by 3310.70. The total ESV in most types of ecosystem service (ES) functions is relatively reduced except for the increase in functions of water conservation, waste treatment, and entertainment and culture. In addition, the change rate of total ESV has been in a high-value agglomeration, and the ES capabilities have been increasing since 2000, while the growth trend of the ES capabilities has been weak, and the high-value agglomeration has been expanding from the core area of Danjiangkou reservoir to the upstream and surrounding areas since 2005. We formulate a WEC scheme according to the partition idea of spatial planning that the priority compensation area accounts for 25.34% of the total study area, and the second priority compensation area, the general compensation area, and the potential compensation area account for 25.34%, 47.48%, and 12.80%, respectively.