Objective To understand the contamination status of microorganisms and pathogenic factors in 19 kinds of food in Zhoushan City, so as to provide basic data for food safety risk monitoring and early warning. Methods A total of 1 246 food samples were collected from 2017 to 2019 according to the requirements of the national risk monitor manual of food contamination and harmful factors from 2017 to 2019. The samples were tested for food microbial pathogenic factors. Results A total of 243 pathogenic factors were detected and the total detection rate was 19.50%(243/1 246). Among them, The detection rate of Salmonella in raw meat was 41.67%(30/72), the detection rate of Vibrio parahaemolyticus in bivalve shellfish was 31.58%(48/152), the detection rate of Anisakid in fresh marine fish was 27.00%(27/100), and the detection rate of Staphylococcus aureus in cold-made pastry was 16.25%(13/80). The detection rate of microorganism and its pathogenic factors in bulk food was higher than that in pre-packaged food. The difference was statistically significant(χ²=92.333,P<0.05). In different sampling locations, the highest detection rate of pathogenic factors was found in farmers' markets (32.54%,150/461), followed by online stores (25.44%,29/114) and small restaurants (23.88%,16/67). Conclusion From 2017 to 2019,19 types of food on sale in Zhoushan City were contaminated by microorganisms and pathogenic factors at varying degrees. The contamination of microorganisms and pathogenic factors in take-out meals,raw animal meat and bivalve shellfish products was relatively serious. It is suggested to strengthen hygiene supervision on these types of food to prevent the occurrence of foodborne diseases.