The Yangtze River Economic Belt development strategy is a new strategy based on the regional harmonious development in our country，through the implementation of infrastructure construction，industry layout optimization，a batch of major projects，such as ecological environment protection to solve the problem of unbalanced development in various regions. And the ecological environmental fair problem is the topic of important strategic thoughts of ecological civilization construction in the “five-in-one” overall arrangements put forward from the 18^th National Congress of the Communist Party of China.PES is the coordination of the regional ecological development of the Yangtze River Economic Belt Area and ecological resource reconfiguration of economic means，is to realize the ecology of the Yangtze River Economic Belt of fair mechanism. Therefore，building mechanism of cross-border PES plays a positive role in coordinating the ecological benefit between the middle and lower reaches of the Yangtze River of the ecological environment governance，natural resources development and ecological engineering construction，and planning as a whole the area of ecological environment protection on fair problems，therefore its urgency is self-evident. However，due to bigger difference in the middle and lower reaches of the Yangtze River Economy Belt of natural resources，geographical location，social economic condition，and building across the eastern，central and western PES mechanism in large area of the Yangtze River Economic Belt faces many problems. This paper reveals the reasons behind the phenomenon. From the building design elements of the，the building path of cross-border PES mechanism in Yangtze river Economic Belt is put forward from aspects on the PES standard accounting，marketing compensation basis and developing the market main body and the PES security mechanism in the Yangtze River Economic Belt. At the same time，combined with the advantages of Shanghai，the countermeasures for Shanghai docking of cross-border PES mechanism of the Yangtze River Economic Belt are put forward，so as to a local experience and the Yangtze River Delta experience are formed and popularized to the Yangtze River Economic Belt.