Hierarchical medical system is the first of the five basic medical systems and is also the ultimate goal to be achieved by the “strong grassroots” of the new medical reform. The implementation of the hierarchical medical system needs the guidance of the scientific and perfect policy system. The research on hierarchical medical system policy is conducive to analyzing the value orientation and evolutionary logic of the existing policies and ensuring that the top-level design cooperates with the social process. Taking the policy of hierarchical medical system published by the central and provincial governments as the study object, the paper establishes a three-dimensional analysis framework of policy instrument, policy objectives, and policy intensity, and explores the internal collaboration of the policy system of hierarchical medical system in China. The results show that the cooperativity of policy tools “supply-demand-environment” is poor, with strong supply, light environment, and weak demand. The cooperativity of “scale – efficiency” of policy objectives is lacking, and the radiation scale of policy objectives at each stage first expands and then decreases. The cooperativity of the policy intensity “administrative effectiveness - content effectiveness” is good, and there is a large space for coordination among the formulation subjects. The cooperativity of the three elements of “instrument-objectives-intensity” is insufficient, and there is a deviation from reality. Especially in the promotion period and breakthrough period, instrument and intensity may not provide strong support for realizing the objectives value. The text of hierarchical medical system policy clarifies the principal-agent relationship between the parties in the medical benefit transmission chain and restricts and guides policy implementation. Therefore, it is necessary to optimize the structure of policy instrument, rationally grasp the policy intensity, coordinate the three elements, and adjust policies closely with the changes in the real situation. The research has important reference value for improving hierarchical medical system policy, promoting the equalization of basic medical services in China, and realizing double breakthroughs in theory and practice.