This paper sets up an intensive management model to control agricultural non-point sources of water pollution the most important contributor in the Taihu water body, according to the principles of micro-economics. We have used GIS as a platform to estimate the arable land and the amount of fertilizer application. By using SPSS correlation analysis on the survey date of local residents, we have conducted a detailed analysis on the economic and environmental benefits of the intensive management. We have estimated that the total nitrogen and total phosphorus emissions decline from the agricultural non-point source is 21 percent and 16 percent than that in 2005. It is concluded that the intensive management can be effectively used to control agricultural non-point sources of pollution in the Taihu Lake Basin. In dealing with the agricultural non-point sources of pollution, we are proposing to fundamentally solve the problem of the agricultural non-point sources of pollution by connecting the social and the actual costs with structural reform in agriculture.