This paper expounds the role of the information flow in each stage of the emergency response, which has to analyzed the accurate description of the information flow in the three emergency stages of the epidemic prevention, and then to reveals the overall evolution of the epidemic situation. Based on the analysis of the epidemic information flow, the paper is proposed the public health emergency response intelligence system for the epidemic prevention., at the same to designed the organizational structure and functional structure from the needs of the epidemic prevention, and in-depth integration of information work throughout the rapid response to emergency of epidemic prevention. The paper is also constructed the theory and method of the epidemic prevention and control information system, combined with the practice of the national epidemic prevention and control mechanism, and the information system has a great role and value in the emergency response to the epidemic. In summary, the research proposes the directions of further breakthrough and implementation for public health emergency information.