Migrants usually exhibit similar or better health outcomes than native-born populations despite facing socioeconomic disadvantages and barriers to healthcare use; this is known as the "migrant paradox." The migrant paradox among children is highly complex. This study explores whether the migrant paradox exists in the health of internal migrant children in China and the role of schools in reducing children's health disparities, using a multi-stage stratified cluster sampling method. Participants were 1,641 student and parent pairs from Grades 4, 5, and 6 of eight primary schools in Beijing. The following school types were included: state schools with migrant children comprising over 70% of total children (SMS), private schools with migrant children comprising over 70% (PMS), and state schools with permanent resident children comprising over 70% (SRS). Children were divided into Groups A, B, C or D by the type of school they attended (A and B were drawn from SRSs, C was from SMSs, and D was from PMSs) and whether they were in the migrant population (B, C, and D were, but A was not). Related information was collected through medical examination and questionnaires completed by parents and children. Prevalence of caries, overweight and obesity, poor vision, and self-reported incidence of colds and diarrhea in the previous month were explored as health outcomes. The results partially demonstrated the existence of the migrant paradox and verified the role of schools in lowering health disparities among children; there are theoretical and practical implications for improving the health of migrant children.