Objective: The paper explores the construction of a multi-level security system for innovative pharmaceuticals in China. Methods: Based on theoretical analysis and policy experience, this paper discussed the role and limitations of basic medical insurance supporting innovative drugs, put forward the importance of the special security mechanism for risk control and financial payment in the initial clinical introduction stage of innovative drugs, and analyzed the characteristics, advantages and disadvantages of the operation modes of commercial medical insurance and special funds. Conclusion: It is of great significance for the development and application of innovative drugs in China to establish a special security mechanism for innovative drugs and clarify its connection and cooperation with basic medical insurance, so as to establish a multi-level security system.