This study aims to evaluate the prevalence and sociodemographic factors of anemia in children <36 months old in China. In this study, data of 24 235 children were investigated from 32 primary health care (PHC) facilities in 11 province-level regions. Pearson χ2-test and logistic regression model were used to estimate potential risk factors associated with anemia. The overall prevalence of anemia was 24.4%, and 32.8% children from rural areas were anemic, but no statistically significant difference was observed between male and female. Predictors of anemia are different regions of China, cesarean delivery, premature birth and neonatal asphyxia. We also found that education level and income of children’s parents are important determinants of childhood anemia. In additional, feeding practice would affect anemia among children aged 6–12 months. Our results could provide some insights for prevention and control of childhood anemia in PHC facilities.