Objective：To understand the present situation of public health emergencies response capacity and preparation in the class Ⅱ and Ⅲ hospitals of Chongqing，to analyze the existing problems，to improve the recognition and response capacity for public health emergencies. Methods：Totally 140 class Ⅱ and Ⅲ hospitals in Chongqing were investigated by using the questionnaire of public health emergencies response capacity of hospitals which was the achievement of Ministry of Science and Technology 863 project. Results：（１）Emergency personnel preparation. 70.3% of the hospitals can ensure the appropriate personnel reserves and 75.4% hired temporary employees or volunteers. （２）Emergency equipment supply and operation ability. 67.2% can obtain emergency equipments from other channels and 24.8% ruled in storage and disposal of the hazardous waste. （３）Emergency supplies reserves. 72.8% had standby emergency resources and 36.8% had drug priority allocation schemes. （４）Emergency method and system. all the hospitals make contingency plans for major infectious diseases and 69.6% had the ability to admit a batch of patients. （５）Emergency communication and collaboration between inter-hospitals. More than 86.4% collaborated with local center of disease control and other hospitals. The emergency equipment supply and operation ability were stronger in class Ⅲ hospitals than in class Ⅱ hospitals（P<0.05）. Emergency communication and collaboration between inter-hospitals was stronger in comprehensive hospitals than in non-comprehensive hospitals（P<0.05）. The emergency equipment supply and operation ability，method and system were stronger in teaching hospitals than in non-teaching hospitals（P<0.05）. Conclusions：The response capacity and emergency preparation already have certain scale in class Ⅱ and Ⅲ hospitals of Chongqing. However，the emergency personnel preparation，equipment supply，disinfection，medical treatment ability construction，communication and collaboration between inter-hospitals need to be further improved.