Ecological compensation is an important measure to promote ecological environmental protection and coordinate the balance of resources and economy. Due to the inequality of resource allocation and economic development in different regions, ecological compensation between regions has become more and more important. However, the basis of regional ecological compensation has been controversial. If the government takes the value of all ecosystem services in the region as the standard of ecological compensation, the compensation amount is too high, and the lack of reasonable compensation mechanism leads to the situation that the ecosystem service accounting research is more and less applied. China doesn't have a regionally comprehensive ecological compensation mechanism now. This study proposes an ecosystem service spillover theory, which deducts the ecological value of spillover after the local ecological service usage as the basis of ecological compensation, and establishes a regionally comprehensive ecological compensation framework. Occupying areas that use other regions' ecological services to develop the economy or over-consume local ecological services provide ecological compensation to compensate or punish their adverse effects on the ecological environment. Overflowing areas that provide ecological services to other regions or abandon the use of local ecological assets to develop economic spillover areas accept ecological compensation to pay or reward its beneficial contribution to the ecological environment. At the same time, taking into account the regional ecological service spillover occupation and economic development level, this study makes 9 kinds compensation plans for different areas. Because of the liquidity of ecosystem services, the ecological compensation recipients and compensators are not one-to-one correspondence. Therefore, the horizontal transfer of compensation funds between administrative regions needs to be coordinated and guaranteed at the provincial or national level. The resulting small surplus is then leveled by the central government or local government through vertical transfer payments. According to the evaluation results of existing ecosystem services, the regionally ecological compensation mechanism established in this paper is used to analyze the ecological compensation payment schemes of 6 typical areas in the Yangtze River Basin, such as Shanghai, Jiangxi and Sichuan and so on in 2015. The results indicated that Qinghai, Sichuan, Hunan and Jiangxi, which need to accept ecological compensation, should receive horizontal transfer payments of 3.226 billion yuan, 15.33 billion yuan, 5.908 billion yuan, and 6.71 billion yuan, respectively. The areas that need to provide ecological compensation are Zhejiang and Shanghai. They should pay a total of 0.197 billion yuan and 4.731 billion yuan of horizontal transfer payments. Since the ecological accounting needs to be oriented to a certain scale or above, the ecological compensation mechanism.