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Water resource (WR) is a complex and interrelated system, which integrates human development and environment. Water price research is gradually carried out under the background of resource economy research, which is an important part of natural resource price research. The main goal of the water price mechanism is to solve the problem of water resource allocation under the pressure of water supply and demand and realize the sustainable development of agricultural economy (AE). Faced with the dual pressure of rising water demand and declining water supply, many regions have begun to reform the water price mechanism and use the CGE model for scientific and reasonable resource allocation. To this end, this paper analyzed the drawbacks and the factors of WR pricing mechanism and used the CGE (Computable General Equilibrium for short here) model to study the upper limit of the pricing of resources, and then analyzed the problems of WR CGE model in agriculture, and finally optimized the problems. According to the experimental analysis, the pricing mechanism of WR under the CGE model can reasonably allocate resources, reduce water demand and promote the development of AE.