Abstract The massive rural-to-urban migration in China has caused widespread separate living arrangements for rural children and their parents. Meanwhile, some children join their migrant parents to live in urban areas. We examined the school disruption of children who were left behind by or migrated with their parent(s) in this paper. Using longitudinal data from the 2010–2014 China Family Panel Studies, we compared the hazards of school disruption between children of migrant parent(s) and children living with both of their parents in rural China. Propensity scores were calculated to control for the probability of having migrant parent(s) and the probability of being left behind for children with migrant parent(s). Findings show that parental migration, especially father-only migration and double-parents migration, raises children’s odds of school disruption in rural China. Remittances and the three-generation living arrangement demonstrate protective effects for children whose father migrates and children whose both parents migrate, respectively. Rural-to-urban migrant children overall are insignificantly different from rural children in non-migrant households. Migrant children show substantially lower risk of school disruption than do left-behind children. Unequal hazards between children of different migration statuses cannot be explained by their variation in guardian-child communication about school life. Findings suggest that the presence/absence of parents is more important than migration itself in affecting children’s school disruption.