To promote the coordinated development and governance of China’s healthcare and medical insurance systems, this paper constructs an order parameter indicator system for the two systems based on synergetics theory. Adopting a cross-system analysis method, it establishes a measurement model for the healthcare-medical insurance compound system, and calculates the order degrees of the healthcare system and the medical insurance system, as well as the synergy degree of the compound system from 2003 to 2023. The results indicate that the development of China’s healthcare and medical insurance systems was generally fragmented during this period, with the synergy degree fluctuating at a low level ranging from -0.09 to 0.10, showing a significant "scissors difference" (asymmetric) evolution characteristic. It is suggested to establish a mechanism for sinking and sharing high-quality resources based on integrated delivery systems (IDS), and use differentiated performance assessments to curb the "siphoning effect" of large hospitals. Furthermore, it is necessary to deepen the reform of diversified compound medical insurance payment methods featuring DRG/DIP, consolidate the global budget and shared savings mechanism, and deeply bind them with the hierarchical medical system. Additionally, a normalized cross-department "medical-medical insurance-pharmaceutical" coordination mechanism and a foundational data-sharing platform should be established. The synergy degree of the compound system should be integrated into a routine monitoring framework to build a dynamic closed-loop governance system.