Natural disasters in agriculture considerably threaten food security and the implementation of the rural revitalization strategy. With the rapid development of new approaches in organizing agricultural production, traditional disaster relief mechanisms are encountering new adaptive dilemmas. Particularly, the active participation of farmers in disaster relief is remarkably insufficient in the context of the reduction in the proportion of agricultural production income. Thus, it is urgent to establish a modernized agricultural disaster relief synergy mechanism. In this study, an agricultural disaster relief synergistic model was constructed with the participation of the government, agricultural service enterprises, and farmers based on the evolutionary game theory, and the strategy interaction law of each subject and its evolution path was systematically analyzed. The following results were revealed: First, the government, agricultural service enterprises, and farmers tended toward an equilibrium state under three different modes. Second, the cost of farmers’ concern and complaint behavior was the crucial driving factor of the three-party synergy. Third, the increasing cost of agricultural service enterprises’ participation in disaster relief significantly affected the evolution path of the system. Additionally, a three-dimensional synergistic optimization path of “incentive-constraint-information” was proposed, laying a quantitative foundation for improving the agricultural disaster relief mechanism and promoting the transition from “passive emergency response” to “active synergy”. This research is of great practical significance to improve the resilience of agricultural disaster response and resource allocation efficiency.