Agricultural supply chain finance plays a vital role in alleviating the financing constraints faced by agricultural business entities in developing countries and promoting inclusive and sustainable agricultural development. However, issues such as high operational risks, weak credit foundations, and insufficient risk safeguards among stakeholders in the agricultural supply chain have hindered its long-term stability. From the perspective of cooperative sustainability, this study develops a tripartite evolutionary game model involving agricultural enterprises, financial institutions, and farmers to explore the behavioral dynamics and evolutionary stability of their strategies. Using the Fuping mushroom supply chain as a case, Matlab-based simulation analysis reveals that the three-party strategy combinations failed to converge to an evolutionarily stable strategy (ESS) but instead exhibited dynamic changes characterized by non-periodic oscillations. Sensitivity analysis further demonstrates that farmers’ credit behavior is a key determinant of the sustainable operation of the supply chain financing system, while enhancing enterprises’ guarantee willingness can effectively mitigate farmers’ default risk. Moreover, stronger cooperative relationships between enterprises and farmers improve the overall resilience and stability of the system. The findings provide practical insights for building sustainable and resilient agricultural financial ecosystems, emphasizing the need to introduce third-party guarantee institutions, strengthen credit constraint systems, and design incentive mechanisms that promote long-term cooperation among stakeholders.