By constructing a comprehensive index of social integration and sub indicators of economic, psychological behavioral and identity integration, establishing simultaneous equations, this paper studies the impact of social integration of migrant population on urban innovation. The results show that the improvement of social integration and urbanization do not improve urban innovation ability, only urbanization based on social integration can promote urban innovation. Economic, social, cultural and behavioral integration have not brought out the improvement of urban innovative ability, and the urbanization level separated from social integration has a negative impact on urban innovation. However,the interaction of urbanization and four dimensional social integration has a positive impact on the level of urban innovation. The level of human capital and city size, as well as the interaction between the two variables and social integration, are all conducive to improving the level of urban innovation, which indicates that at the same level of social integration, groups with a higher level of human capital have a greater impact on urban innovation ability. At the same time, compared with small and medium sized cities, the improvement of social integration in mega cities and super cities has a greater impact on urban innovation ability.