Abstract: Objective To conduct public health risk assessment of flood disaster, determine the public health priority at present, and provide scientific evidence for the preparedness of public health emergency response. Methods The public health problems caused by flood disaster were found through literature review and expert consulting, and Delphi method was used to screen public health problems. Australia/New Zealand risk analysis model was used to construct the hierarchy model and evaluate the judgment matrix. The weight of each layer and the total weight, and sort the weight of problems were calculated. Results The highest risk caused by flood disaster was food poisoning, followed by skin disease, in Anhui in 2016, the other risks included injury, acute conjunctivitis, the other infectious diarrheal disease, schistosomiasis, bacterial dysentery, epidemic hemorrhagic fever, leptospirosis and cholera. Conclusion According to the result of risk assessment, the different public health emergency response preparedness should be carried out to address the risks at different stages.