Objective To understand the content and distribution characteristics of heavy metal in food in Chongqing, analyze and evaluate the risk, and provide scientific basis for food safety assessment and targeted control measures in Chongqing. Methods With multi-stage stratified random sampling method, Chongqing was divided into four areas. A total of 1 800 samples within eight food categories with large consumption were collected in the whole city with 450 samples from each area. The single factor pollution index method and the Nemero comprehensive pollution index method were used to evaluate the degree of heavy metal pollution in food. Results Among the eight food categories in this study, all the average heavy metal contents were lower than the national standard limit. The highest median(P50) contents of cadmium, arsenic and mercury in edible fungi and their products were 0.230,0.150,0.012 mg/kg, respectively. The median contents of cadmium (0.023 mg/kg) and arsenic (0.055 mg/kg) in cereals and their products were the highest, and the mercury contents of aquatic animals and their products (0.004 mg/kg) were higher than other food categories. The single factor pollution index and Nemerow comprehensive pollution index were used to evaluate the heavy metal content of eight categories of food. All kinds of food could be evaluated as safe and slightly polluted. However, some samples of edible fungi and their products had higher heavy metal content and higher comprehensive pollution index. Conclusion Eight categories of foods in Chongqing had different levels of heavy metal pollution, but the overall pollution level was relatively low. Some samples of edible fungus and its products had high level of heavy metals and high comprehensive pollution index, so it is necessary to further strengthen targeted control measures.