Based on the data of CMDS2017 and guided by Sen’s welfare theory, this paper discussed the influence mechanism of residence certificate system on migrant workers’ willingness of citizenization. It is found that migrant workers’ willingness of citizenization is generally optimistic, and that of the new generation is better than the old one. Residence certificate system has a direct positive effect on migrant workers’ willingness of citizenization. Compared with migrant workers without residence permit, those with residence permit have stronger willingness of citizenization. The residence certificate system also indirectly improves migrant workers’ willingness of citizenization by positively influencing their multiple welfare, mainly economic conditions and social opportunities, but there are some differences between the new and old migrant workers. Therefore, we should continue to optimize the welfare system based on residence certificate system, and take into account the intergenerational needs, so as to speed up identy change from migrant workers to urban residents.