Background: a few studies have been conducted which describe health status of Migrant Peasant Worker’s children. However, there are no studies which compare physiques of MPW’s children with those of rural children and urban children. Also, few studies have been done on physiques of MPW’s children as it relates to socioeconomic factors in China. Methods: We examined across-sectional study of 2457 children from Shanghai and Wuhu city in 2011. First, we compared the differences of physiques among three groups by ANOVA. Second, ANCOVA were applied to analyze the associations between the physiques and socioeconomic factors by taking physiques as dependent variables. The independent variables included socioeconomic factors such as the parental occupation, the parental education and family monthly income. Third, ANCOVA were used to assess differences in physiques among the three groups by adjusting socioeconomic factors. Results: There were significant differences in all physical indexes, no matter they were boys and girls (P < .001). Children’s physiques of MPW were smaller than those of children of Citizen in Shanghai City. Among all ages, regardless of gender, Children’s physiques of MPW were bigger than those of children of rural resident. In both boys and girls all indexes displayed statistically significant associations with parental occupations (P < .001). There were strong associations between parental education and all physical indexes (P < .001). Family monthly income was found to be significantly associated with children’s physiques (P < .001). In both boys and girls, there were strong associations between physique and group in all indexes (P < .001), but physiques hardly had any associations with socioeconomic factors. Conclusions: We find that physiques of MPW’s children were smaller than those of children of citizen in Shanghai City, and physiques of MPW’s children were bigger than those of children of rural resident. There are strong associations between physiques and socioeconomic factors.