This paper focuses on the sustainable development dilemma of agricultural production in China under the pattern of intensive management, which is seriously challenged by agricultural non-point source pollution. The key to effectively break through the dilemma is to promote the co-governance of agricultural non-point source pollution control by stakeholders including local governments, new agricultural operators and traditional farmers. Accordingly, this paper discusses the interactive decision-making relationships between new agricultural operators and traditional farmers under the guidance of local governments, by constructing a trilateral evolutionary game model, as well as analyzing evolutionary cooperative stability strategies and realizing the simulation of evolution processes in different scenarios by MATLAB. The results show that new agricultural operators play a leading role in agricultural non-point source pollution control, whose strategies have effects such as technology spillover. The rewards from the superior government will support local governments in taking proactive action in the co-governance of agricultural non-point source pollution control, and then local governments can offer technical support and subsidies to new agricultural operators and traditional farmers for reducing their costs. Furthermore, this paper also finds that there are green synergy effects among the groups, where the variations of parameters and strategies by one group would affect the two others. Additionally, agricultural land operation rights transfers would cause traditional farmers to take more time to cooperate in the co-governance of agricultural non-point source pollution control. In order to promote the multi-agent co-governance of agricultural non-point source pollution control under intensive management pattern, this paper suggests that it should be necessary to reduce their costs and improve incentives, as well as to increase the common interests among groups and enhance their green synergy effects.