Household register system reform is the key to the reform of China’s dual system between urban and rural areas and to narrowing the dual disparity, and using household register system reform to boost China’s social system reform is the focus of social system reform of China in coming thirty years. Chongqing’s using household register system reform of migrant workers to advance overall urban and rural comprehensive development reform is a model and an experiment of China’s social system reform. However, urban and rural dual system is a huge system coupled with each other, there is interactive constraint between the systems, and meanwhile, the institutional reform implicates huge reform cost. On the one hand, Chongqing should boost household register reform of migrant workers in proper sequence, on the other hand, on the basis of existed land system, rural endowment insurance system, rural medical insurance system, rural education system and so on, Chongqing should work out new systems such as rural retirement and endowment insurance system, rural contracted land quitting system after retirement and rural housing insurance system so as to provide necessary financial support for migrant workers to become urban residents, weaken and eliminate psychological barriers for the migrant workers to become urban residents because of system factor.