Intervention of online public opinion, especially agricultural rumors, has increasingly become an important issue that is related to the online society safety and reflecting the managers’ social management capabilities. In this paper, meta-synthetic methodology was used to investigate the intervention mechanism of online public opinion system. General characteristics of online public opinion system were characterized qualitatively, and an opinion supernetwork model was built to analyze the intervention mechanism quantitatively. We put forward a rumor intervention mechanism including intervention timing, intervention mode, and intervention intensity. Based on system modeling and simulation, an agricultural rumor case was used to verify the practical effects of online agricultural rumor intervention. The results show that rumor intervention based on meta-synthetic methodology produces good results. This investigation will help to provide a reliable basis for the development of more sophisticated and effective rumor intervention strategies.