Taking bus and subway into account, an asymmetric polycentric urban system equilibrium model is constructed to explore the impacts of rail transit on the distribution of residents and labor force in a linear polycentric urban system. By comparing the urban system equilibria before and after the introduction of rail transit, the influence of rail transit on urban performance is analyzed. The results show that the introduction of rail transit makes the advantaged center more attractive for the labor force, and further widens the economic level gap between the two business centers. Specifically, larger distance between the two commercial centers and the higher subway travel cost would strengthen the polarization effect caused by rail transit investment. Since the improvement of transportation makes it easier for residents to accept long-distance commuting and they are more willing to choose the jobs in the advanced center.