Agricultural non-point source pollution has the characteristics of complex occurrence mechanism and wide space-time range. The randomness of the time and place, occurrence of intermittent mode, uncertainty of emission form and way have increased the difficulty of agricultural non-point source pollution prevention and control. Based on the analysis of three stages of agricultural non-point source pollution prevention and control, the characteristics of the renewable energy technology and its specific methods of fusion technique combined with agricultural non-point source pollution prevention and control system were described in detail in this paper. Meanwhile, the scarcities of renewable energy technology applied in agriculture non-point source pollution prevention and control were pointed out and the important role of the renewable energy technology in agriculture non-point source pollution prevention and control were emphasized. According to this, this paper aimed at the deficiency of biogas technology and monitoring methods, two kinds of specific solutions were proposed and the advantages and disadvantages of two kinds of schemes were analyzed, respectively. The research work in this paper is of great guidance for the renewable energy technology applied in future agricultural non-point source pollution.