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Agricultural non-point source pollution causes global warming and the deterioration of air and water quality. It is difficult to identify and monitor the emission sources of agricultural pollution due to the large number of farms in China. Many studies focus on the technological aspect of achieving agricultural sustainability, but its socioeconomic aspect is poorly understood. Here, we report how group size (number of farms in a certain region) affects agricultural pollution governance through conducting a social science experiment. We found that when communication was allowed among group members, a small group size facilitated cooperation. Although deviations from the cooperation equilibrium occurred with time in all groups, the smaller the group size, the slower the cooperation equilibrium became frangible. These findings suggest that reducing number of farms and extending the length of farm property rights can benefit the mitigation of agricultural non-point pollution in China. Social science experiments can be a useful tool to understand the socioeconomic aspect of agricultural sustainability.