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Based on the current state of China’s agricultural industry, this article proposes an integrated framework for the agricultural innovation ecosystem in developing countries. Furthermore, a dynamic simulation model is constructed to analyze the game process and factors influencing the agricultural innovation ecosystem. The results indicate that industry-university-research collaboration serves as the main source of innovation within the agricultural innovation ecosystem, playing a central role in its development. The willingness to participate, cost of participation, and establishment of default fees by governments, agro-related enterprises, universities, and research institutions have significant implications for the evolution of collaborative innovation within agricultural innovation ecosystems. In order to promote the evolution of the system, agriculture-related enterprises, universities, and research institutions should establish more effective reward and punishment mechanisms, as well as cost control mechanisms. Governments should set reasonable regulatory costs and incentive intervals to actively foster a collaborative innovation atmosphere. The innovation points of this paper are as follows: extending the theory of innovation ecosystems to agriculture, particularly in developing countries characterized by imbalanced and insufficient development. A game model is also constructed to represent the collaborative innovation evolution among government, agriculture-related enterprises, universities, and research institutions, with the government as the endogenous variable. Through numerical simulation, the dynamic evolution process of collaborative innovation within the agricultural innovation ecosystem is revealed. This research enriches and expands upon innovation ecosystem theory, providing guidance for the of innovation ecology in agriculture through mathematical models in developing countries. This, in turn, promotes the convergence of symbiotic, shared, and-creation development.