School-enterprise cooperation and innovation is an essential support for the implementation of an innovation-driven development strategy. This study examines the stages of school-enterprise cooperation and innovation, underpinned by integrated media, through the lens of deep coupling theory. It categorizes the process into pre-, mid-, and post-stages. The pre-stage involves analyzing university agricultural programs to develop a credit network database identifying optimal school-enterprise pairings. The mid-stage focuses on enhancing knowledge exchange mechanisms to tightly integrate participating entities. The post-stage assesses the impact of these integrations, revealing a coordination degree of 0.416 among agricultural majors, suggesting that effective interaction mechanisms are yet to be established, occasionally leading to mutual constraints. This research informs strategies to foster robust school-enterprise collaborations in agricultural education.