Objective To explore the capacity for health emergency at county-level in Anhui province and provide scientific suggestions and proofs for the government to establish the strategy. Methods The questionnaire was designed by national health and family planning commission. We made a cross-sectional study on basic situation of emergency public health response by the questionnaire in 104 counties in Anhui. A capacity in public health emergency response evaluation model was developed using the factor analysis. Results A county level capacity in public health emergency response evaluation model was developed based on the factor analysis as follows: C=0.698C₁+0.179C₂+0.123C₃, where C is a total score,C₁ is a capacity score for preparedness of public health emergencies,C₂ is a capacity score for detection an aftermath emergencies,C₃ is a capacity score for disposal. Total capacities, preparedness, detection an aftermath in public health emergency response of county-level CDC were better than that of district-level CDC. And there was statistically significant. Conclusion A factor analysis, combined with the capacity for health emergency of county-level's evaluation results is scientific and feasible, which can provide reference for evaluation and management of the health emergency capability.