The harm caused by defective vaccines to human health and social stability is immeasurable. Aiming at the government’s supervision of the vaccine market, an evolutionary game model is constructed to analyze the quality of supervision and the key factors in the dynamic interaction between government departments and vaccine manufacturers under different supervision modes in the vaccine manufacturing process. The results show that: (1) Severe punishment by government regulatory authorities, and increased costs of rectification after investigation and handling of involuntary behaviors of vaccine enterprises can effectively prevent involuntary behaviors of vaccine enterprises. (2) In the early stage of the game, the success rate of the government’s efficient supervision will make the vaccine enterprises continuously self-disciplined; when the vaccine market is relatively stable, the government’s supervision departments tend to be more conducive to passive supervision. (3) The success rate of government regulatory departments and the probability of a third-party reporting to play a great role in promoting the self-discipline of enterprises. (4) The power of government and regulation are conducive to promoting the active supervision of the government regulatory authorities but corruption of government and awareness of people are different. Once the phenomenon of vaccine enterprises’ non-discipline increases, the government regulation must change from passive regulation to active regulation. Therefore, the government should implement different measures according to the characteristics of each period in the manufacturing process to effectively prevent problematic vaccines. The conclusions and policy recommendations are significant for addressing the issue of insufficient self-discipline of vaccine manufacturers.
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