Objective To provide data basis of foodborne disease control， the pathogen of foodborne diseases in Chongqing， dietary history and the source of food were analyzed.Methods The information of foodborne disease cases in 27 sentinel hospitals in Chongqing from 2019 to 2020 were collected. Stool specimen or swab from foodborne disease cases was collected to detect Salmonella， Vibrio parahaemolyticus， diarrheagenic Escherichia coli， Shigella and Norovirus.Results Four thousand two hundred and ninety four diarrhea cases were collected. The positive rate of pathogens was 12.09% （519/4 294）， including 5.33% of Norovirus， 4.66% of Salmonella， 1.96% of diarrheogenic Escherichia coli， 0.12% of Shigella and 0.02% of Vibrio parahaemolyticus. The pathogen detection rates were higher in the second （18.50%） and third （13.00%） quarter than others and obviously peaked in summer and autumn. The highest pathogen detection rate was 19.19% （71/370） in 0-1 years old group. 4 289 of 4 294 cases provided suspicious diets information， among which were mainly meat and meat products 19.26% （846/4 289）， grain and grain products 17.65% （757/4 289）， 58.27% （2 502/4 289） of the foods were homemade， 30.64% （1 314/4 289） were from catering service industry， 55.42% （2 377/4 289） of the food came from family， restaurants accounted for 12.17% （522/4 289） and retail stores accounted for 10.91% （468/4 289）.Conclusion Norovirus and Salmonella were the main pathogens of foodborne illness cases in Chongqing， and the suspicious food was mainly homemade from family sources. It is suggested to strengthen food safety supervision in summer and autumn with high incidence of foodborne diseases， focus on 0-1-year-old infants， and carry out family food hygiene and safety knowledge education. To provide technical support for effective prevention and control， the active monitoring of foodborne diseases should be strenghened.