Food security is a cornerstone of national development, and farmland protection and rationale are crucial for its assurance. However, integrating primary, secondary, and tertiary industries (IPSTI) in rural areas places significant pressure on farmland, threatening food security. This paper employs an evolutionary game model to explore how effective IPSTI can be achieved through stakeholder cooperation, ensuring rational farmland use under strict protection policies. The results reveal eight local equilibrium points in the game model, which can achieve asymptotic stability under varying conditions. Additionally, the behavioral parameters of local governments significantly impact their regulatory strategies for the non-agricultural use of farmland. When benefits increase, or penalties are strengthened, local government regulatory initiatives increase, constraining the behaviors of other participants. The village committee’s support strategy is influenced by benefits and costs, requiring a balance between promoting local economic development and minimizing non-agricultural use of farmland by enterprises. Enterprises’ decision-making primarily depends on the trade-off between the benefits and costs of non-agricultural use of farmland. The core findings of this study provide a crucial theoretical basis and decision support for formulating farmland protection policies and promoting industrial integration.