An important feature of population migration is the strengthening trend of family migration. Whether children migrate with their parents or not will not only affect the happiness of families, but also reflect the speed, structure and quality of China’s urbanization. Due to the limitation of the dual urban-rural division of the household registration system and the defects of the housing system design, it is still common for the children of migrants to be left behind. This paper studies the effect of affordable housing on children’s migration by using the data of China Migrant Dynamic Survey after considering the rare event bias and endogeneity bias. The study shows that affordable housing can reduce the negative impact of quitting the labor market and rent growth due to children’s migration, and increase the possibility of children’s migration. Nevertheless, in China’s two-system housing market structure, the supply of affordable housing has a threshold effect on the migrants. The overall level of affordable housing availability is relatively low. Meanwhile, under the effect of " social shield” produced by the household registration system, the rural migrants are more affected by institutional factors and rely more on affordable housing in the family migration process. This paper reveals the matching contradiction between the transition of migration pattern and housing supply in the population urbanization process, and clarifies that the deep impact of institutional constraints on the effective supply of affordable housing is expounded. It provides useful enlightenment for the current new round of housing system reform to increase the public housing supply to the migrants, and to establish a new housing security supply system.