Background: The outbreak of a disease is presenting a serious challenge to China’s current public health emergency management system. Despite of China’s emergency preparedness is showing a good overall progress, gaps remain in the implementation of effective early warning system.Methods: In this context, a tripartite evolutionary game model composed of the local government, the whistle-blower, and the public is formulated. By using MATLAB, the dynamic evolution path of the game model is stimulated under different conditions. The stable strategies for early warning system for public health emergency are also explored. Results: The results indicate that the cost of whistleblowing, the cost of response, and the benefit of attention significantly influence strategic decisions among three parties in the process of managing public health emergency. When there is a serious risk of an outbreak, the local government tends to adopt a active response strategy in the first instance to try to reduce the loss of life and property, whilst the cost of public warning to the whistleblower may influence government’s decision-makings. When the accuracy of early warning information is questionable, the local government tends to adopt a cautious strategy to reduce the total loss to society. Nevertheless, the whistleblower may choose to give early warning signs to the public, given the potential risks to the public. As a group with limited information resources, the public’s strategic decisions are largely influenced by the actions of the local government and the whistle blowers. The whistleblower thus faces a dilemma in public health early warning system.Conclusions: This study highlights the importance of the whistleblowing in managing public health emergency. Yet our findings provide theoretical support for policy recommendations for promoting the public health emergency preparedness.