In this paper we analyze all levels of government’s activities in non-point source pollution treatment in rural areas from the perspective analysis of economics by starting from the economic characteristics of non-point source pollution in rural areas, besides, we discussed the dilemma between the rules and regulations of the central government when preventing and controlling the non-point source pollution in rural areas and the producers’ behaviour which is protected by local governments. Thus we derive the government should reduce the direct administrative intervention, meanwhile by using more economical methods and incentive mechanisms which can control the input of natural resource and the output of the pollutants in the course of non-point source pollution treatment in rural areas, the market price system of green organic agricultural products will be formed, which will lead the behaviour of producers and consumers to beneficial to environment.
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