Ecological compensation standards and the allocation of compensation funds have always been the core issues of watershed ecological compensation. Due to the construction of the Eastern Route of the South-to-North Water Transfer Project (SNWTP), Jiangsu Province has paid a huge cost for the protection of water resources, and local economic development has been greatly affected. Therefore, this paper takes Jiangsu Province, the water source area of the Eastern Route of the SNWTP as an example, and combines a geographic information system (GIS) and remote sensing technology, using the ecosystem services value method to calculate the ecosystem services value of Jiangsu Province from 2005 to 2018. Then the change of this ecosystem services value in Jiangsu Province from 2015 to 2018 is taken as the basis for watershed ecological compensation standards of the Eastern Route. Through a compensation fund allocation model, watershed ecological compensation funds are allocated to four cities, Yangzhou, Huai’an, Suqian and Xuzhou, which are located along the Eastern Route of this SNWTP in Jiangsu Province. The results show that: (1) The ecosystem services value of Jiangsu Province has changed greatly. Urbanization and market environment of grain crops are the main reasons for this change; (2) the relationship between ecosystem services in Jiangsu Province is mainly synergistic; (3) Suqian receives US$24.73 million; Huai’an receives US$16.49 million; Yangzhou receives US$54.88 million and Xuzhou receives US$0.95 million in watershed ecological compensation, respectively. Watershed ecological compensation standards based upon the value of ecosystem services, and the allocation of compensation funds at the municipal level, are conducive to the improvement in efficiency of watershed ecological compensation in mainland China.