To analyze the incidence of eating problems and risk factors in children aged 1-6 years, and provide evidence for formulating relevant prevention and control strategies. From June to December 2019, two community health service centers and two kindergartens were randomly selected in Shunyi district of Beijing by using stratified random cluster sampling method. Self-designed questionnaires were used to collect data on individual information, family information, and the incidence of eating problems and related factors. Multivariable logistic regression analysis was conducted to identify related factors. A total of 2 391 valid questionnaires were returned, the analysis result indicated that 1 432 children had at least one eating behavior problem, the incidence rate was 59.9. The most common eating problem was inattention while eating (48.8), followed by irregular eating position (14.0), picky eaters (13.0), excessive eating time (11.2), excessive snacks intake (9.0), and soup with rice (4.6). The mother's education level, family income level, main caregivers and family members' attitudes toward child's eating were related factors for eating behavior problems in children. Mothers with high education level (=0.528, 95: 0.431-0.647) and family with high income level (=0.656, 95: 0.473- 0.909) were the protective factors for child's poor eating behaviors. Grandparent caring (=1.366, 95: 1.151-1.622), coaxing or forcing child to eat (=1.581, 95: 1.284-1.947) were the risk factors for child's poor eating behavior. The incidence of eating problems was high in children aged 1-6 years. It is necessary to strengthen the intervention in families with low-income and low-education levels and children raised by grandparents to reduce the incidence of poor eating behaviors in children.