Objective To explore the capacity for health emergency at prefecture and county level in Anhui province and provide scientific suggestions and proofs for the government to establish the strategy. Methods CDCs, administrative departments of public health, health supervision department, hospitals at prefecture and county level in Anhui province were surveyed by questionnaires. Results All of the prefecture and county level governments had involved health emergency system construction into the national economic and social development planning, and had special fund for health emergency daily work. Among 106 units, 45% had set up separate department of health emergency office and all prefectures and counties formed the health emergency response team. The rate of health emergency stockpile management system was 67% and staff training rate was 65%. 90% of them had carried out the propaganda work of health emergency. The indicators for the health emergency were reaching 95% and all of them could effectively dispose health emergency. 46% had established expropriation of material return and compensation system and health emergency workers subsidy system. The average score of the prefectures, counties and districts were 716, 695 and 601, respectively. The score of emergency response team and the health emergency disposal had high score, which were higher than 75% of the total score. There were statistical differences on comprehensive score of health emergency ability except for equipment reserve and training. Conclusion The health emergency system in Anhui province has been basically established, but there is still a gap with national assessment standards. Therefore we should further improve the health emergency system and strengthen equipment reserve and rehabilitation mechanism. Establishing the health emergency demonstration county in whole province is our next work focus.