Abstract: Migrant workers flowing between urban and rural are special in the choice of health institutions. We obtain the data from 502 questionnaires for migrant workers in Nanjing and use the method of multinomial logistic regression. The data analysis finds: the community hospitals are the migrant workers’ first choice and nearly half of the migrant workers will go to the county hospital and the better hospitals when they get sick. The factors that influence the choice of health institutions are mainly the socioeconomic status and health condition of the migrant workers. In order to ensure that everyone will have access to basic medical service, the government should make efforts on health education, medical service and medical insurance.