The global ecology movement of the 1960s gave rise to international efforts to of farmland ecological protection. In these systematic, multi-agent projects, the long-term viability of farmland ecological protection rests significantly upon the alignment and synergistic interaction of the primary agents involved. Beginning in 2017, the Chinese government prioritized farmland ecological protection, instituting a collaborative governance structure involving policymakers, policy implementers, and agricultural producers. To appraise the characteristics of this structure, this study develops a multi-agent theoretical framework according to a “motivation-behavior” model for farmland ecological protection. Analyzing the motivations of these agents and the resultant synergy across the 2000–2020 period, this research indicates a significant rise in the motivation of Chinese policymakers toward farmland ecological protection, coupled with a significant decline in motivation among agricultural producers. Policy implementers’ motivation, however, has remained consistent. Employing a coupling and coordination model to assess the collaborative effectiveness among these actors, this study identifies a downward trend in synergistic effectiveness across three phases: primary coupling, approaching decoupling, and mild decoupling. To further explore the collaborative effectiveness of policy implementers and agricultural producers, a Tapio decoupling model is utilized to analyze changes in their synergistic activity. The temporal analysis of motivational shifts indicates a stabilizing trend among policy implementers and fluctuating efforts from agricultural producers. Spatially, high-value areas for policy implementers have experienced a significant decline, migrating from the left to the right of the Hu Line; whereas, high-value areas for agricultural producers have steadily decreased. Specifically, areas where synergistic efforts between implementers and producers in farmland ecological protection are being observed have expanded, while areas exhibiting decaying synergy have contracted. Areas initially indicating synergy decay demonstrate an initial increase followed by a decrease. This study concludes that China must develop a compensation structure for farmland ecological protection targeted at business actors, execute region-specific protection plans, and strengthen multi-agent motivation to cultivate more robust synergistic outcomes.