Being overweight or obese is one of the public health concerns worldwide, and its prevalence is gradually increasing. Obesity has been proven to be associated with some cancers, including upper gastrointestinal cancer (UGC). However, studies on the prevalence of obesity among residents of areas at high risk of UGC in China are minimal. The aim of this study is to assess the prevalence of obesity and its influencing factors among people aged 40–69 years (high-risk population) in high-risk areas for UGC in Jiangsu Province, southeast China. This cross-sectional study involved 45,036 subjects aged 40–69 years identified in the Rural Early Diagnosis and Treatment of UGC Project database in Jiangsu Province from 2017 to 2021. Differences in prevalence across gender and age were assessed using the Chi-square test. Using a multinomial logistic regression model, we examined independent risk factors for overweight/obesity and their gender and age differences. The prevalence of overweight, obesity, and overweight/obesity varied based on the standards used: Chinese standard (42.1%, 11.9%, and 54.0%) and WHO standard (34.7%, 4.7%, and 39.4%), respectively. Being overweight was more common in men than women, while obesity was more common in women than men. Age of 50–59 years, married, household size of 7–9, drinking, soy products, pickled food, and hot food intake were positively associated with overweight/obesity. Females, 60–69 years, higher education level, household size of 4–6, annual family income of more than 60,000 CNY, smoking, and fresh fruit intake were negatively associated with overweight/obesity. Stratified analysis showed that the effects of age, education and meat, egg and dairy products on overweight/obesity were different across gender. The impact of fresh fruit and vegetables on overweight/obesity was also heterogeneous between the younger (40–59 years) and older (60–69 years) groups. In conclusion, the prevalence of overweight and obesity is high among adults aged 40–69 years from high-risk areas for UGC of Jiangsu Province, southeast China. Independent influencing factors of being overweight/obese included gender, age, marital status, education, household size, annual family income, smoking, drinking, fresh fruit, soy products, pickled food and hot food intake, and may vary by gender and age. Screening-based interventions should be considered to control obesity levels among screened participants. Besides, heterogeneity of influencing factors across subgroups could be focused on to improve intervention effectiveness.