Rural–urban migrant children are a rapidly growing population in Chinese cities. There is emerging literature on the educational inequality faced by migrant children, but most studies focus on their educational performance or attainments and use non-migrant children with non-agricultural hukou in urban areas as one single reference group. This paper argues that Chinese society is segmented by both hukou type and location, and examines the educational aspirations of migrant children from the perspective of segmented assimilation theory. On the basis of the 2013–2014 wave of the China Education Panel Survey, the results show a segmented assimilation pattern: migrant children with non-agricultural hukou had a similar likelihood of aspiring to tertiary education or above; whereas migrant children with agricultural hukou showed higher aspirations of completing at least tertiary education, and the disparity remained significant after considering family resources and school segregation. In family resources, social capital, in form of social communication with parents, benefited migrant children’s aspirations more than it did for their non-migrant counterparts, regardless of their hukou type. In school segregation indicators, academic segregation channeled migrant children with agricultural hukou to a less desirable condition. These findings carry practical and policy implications for understandings of migrant children’s educational aspirations.