To assess the epidemiologic investigation capacity to food safety incidents among prefectural and local CDC in Guangdong Province and provide references for health emergency management strategies and training programs planning.Methods Related institution chiefs of 124 prefectural and local CDCs in Guangdong Province were interviewed by E-mail with a questionnaire, which contained 35 items and four parts including staff composition, education and training, emergency response, and financial support. Results It was shown that the staff composition was basically reasonable, while staff numbers were generally limited. Compared with non-Pearl River Delta region, CDC staffs in Pearl River Delta region had more FETP training opportunities. Most prefectural CDCs and local CDCs had their own emergency plans, but never trained. For technical manuals or standards, the ratio of training would be higher. Case interview questionnaires were all prepared, but not unified. Most CDCs were equipped with sampling tools in the field and supplemented periodically, and Pearl River Delta region CDCs were equipped better. Information resources of food safety incidents were mainly from hospitals (74.2%). Task orders of food safety incidents were mainly from DOH (79.8%). Results of simulating case interview suggested the field epidemiology capacity, such as confounding factors eliminating, analytic epidemiology, statistical analysis and process, specimen collecting and testing items confirming, need to be improved greatly, especially in the local level. Great financial gaps for epidemiologic investigation of food safety incidents generally existed in CDCs. The ratio of financial funding from government in prefectural CDCs was 82.8% and local CDCs was 64.1%.Conclusion Staff and financial gaps, epidemiology capacity and differences among regions are very common in prefectural and local CDCs of Guangdong Province. The government should enhance the staff and financial support. CDCs should enhance the development of epidemiology investigation capacity to food safety incidents.