BACKGROUND: Although many previous epidemiological studies have reported the incidence of diseases, mortality rate and economic losses after natural disasters, none of these studies has been comprehensive enough. Our aim was to establish a synthetic evaluation model (SEM) that can be used to analyze flood hazards. METHODS: Initial evaluation indicators were selected using systematic and literature data analysis. These indicators were tested with single or multiple variable analyses. Final evaluation indicators and their weights were determined using the Delphi procedure. We established a SEM of flood hazards using the hierarchy method and tested the model using jack-knife analysis. RESULTS: The SEM on flood hazards consists of 6 first-rank indicators and 24 second-rank indicators. First-rank indicators were: direct casualties (w = 0.2123), the increased incidence and prevalence rate of the disease (w = 0.1715), excess mortality rate (w = 0.1745), mental injury (w = 0.1038), epidemic focus expansion (w = 0.1572) and economic loss (w = 0.1807). The agreement of the model reached 98.2% tested with the jack-knife analysis. CONCLUSION: A SEM of flood hazards was established with an agreement of 98.2%, which can be used to evaluate the hazards, and assist public health-care workers provide appropriate flood disaster management.