This paper, from the city integration perspective, analyzes the main beneficiaries who benefit from the household registration system reform, and studies the influence of individual decisions about the transfer from agriculture to non-agriculture. Based on it, this paper makes an empirical research by using the survey data about migrant workers in Chongqing. The research findings are as follows: (i) The urban employment, the living condition and the rural connection have a significant impact on migrant workers’ transfer decision; (2) If the value of those factors (such as the working stability, the family income, the urban house condition and the urban social security) is higher, then the migrant workers who have no economic interest in rural areas are better able to integrate into the urban areas, therefore the inclination to transfer the household registration from agriculture to non-agriculture will be much stronger. It is proposed that we should do some significant things, such as enhancing the investment of security housing, bringing the migrant workers into the city housing accumulation fund system and giving them prior allocation right, perfecting land elastic exit mechanism, creating a harmonious employment environment, which are important strategies promoting migrant workers to integrate into the urban areas and affecting their individual decision about transferring from agriculture to non-agriculture.