Promoting the social integration of rural-urban migrants in metropolis plays a vital role in accelerating the process of people-centered new urbanization. It is also the core content to improve the mechanism of rural-urban integration and development. Besides, providing proper housing for these migrants is the prerequisite for their residence and career development in inflow areas, which will perform a fundamental guarantee to promote their overall integration into destinations. However, due to the high housing prices and the limitation of initially-endowed capital accumulation, rural-urban migrants cannot easily purchase the owner-occupied housing in inflow areas. In a sense, they show significant disadvantages in “housing resources” compared with urban residents, and alternatively reside in rental housing. This paper aims to study the impact of housing rent on the social integration of rural-urban migrants by using the 2017 China Migrants Dynamic Survey (CMDS). It finds that high housing rent in inflow areas can significantly inhibit the social integration of rural-urban migrants. In addition, the impact of housing rent presents significant heterogeneity across individual demographic characteristics, household characteristics, and leasing types. Furthermore, this paper also figures out that improving the housing affordability of rural-urban migrants can effectively promote their social integration in their destinations. Particularly, the provision of flats from working units (employers) can significantly weaken the negative impact of high housing rent on the social integration of rural migrants. Based on these findings, this paper provides several contributive implications to policy-makers. For those cities with large influx migrants, it is necessary to revitalize the existing housing resources and increasingly supply affordable rental housing to optimize the structure between demand and supply in the housing market. It is also necessary to conduct a series of supportive policies such as financial subsidies or tax incentives for affordable housing suppliers. Compared with previous literature, this paper highly focuses on city-level housing rent and its influence mechanism on the social integration of rural-urban migrants from the perspective of housing affordability. Besides, this paper clarifies the relationship between the development of housing rental market and urban livability and attractiveness. Additionally, it re-thinks the potential problems of China’s urban housing rental market from the perspective of the social integration of migrants. This would be of great help to promote the sustainable development of housing rental market, and provide policy implications to improve the social integration level of migrants and their well-being.