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Ecological compensation (EC) is an important way to solve the imbalance of cross-regional economic development and realize regional coordinated development. How to quantify the standard of EC has become a hot research topic. Firstly, this paper selected the Three Gorges Reservoir Region (TGRR) as the study area, and constructed a cross-regional spillover ecological value measurement model based on the extended emergy analysis. From the perspective of the “ecology–economy–society” complex ecosystem, this paper used emergy to reflect the social, economic, and ecological function and service value of the TGRR, and estimated the ecosystem emergy supply and consumption in the TGRR. Then, comparing the watershed ecosystem emergy supply and consumption, we can judge the status of the ecological surplus and deficit of the TGRR, and transfer the spillover ecological emergy to spillover ecological value (SEV) by using the emergy currency ratio (ECR). Finally, combined with different actual payment level coefficient, we can obtain a relatively objective and robust compensation standard. The results show that the SEV of the TGRR in 2016 is 2.70 × 1011 USD, which indicates that the TGRR is in the state of ecological surplus. The TGRR should get EC about 2.85 × 1011 USD according to the ECR. Based on the research results, it is suggested to expand the transfer payment to the TGRR. At the same time, it is suggested to formulate different ecological compensation standard (ECS) according to regional differences, which has important practical significance to establish the allocation standard of EC, and provides a typical case basis for other large reservoir areas or typical reservoir areas.