We establish the two-sector economy model including the urban sector and the rural sector, derive the labor demand curve of the urban sector and rural sector under the condition of balanced production decisions with benefit maximization, and analyze the labor flow when in the short-term or long-term two-sector economic equilibrium. The results show that rising wages caused by short-term internal and external impact increases the pressure on the employment in two sectors, and the urban sector is difficult to absorb the surplus labor of the rural sector. However, under the conditions of free flow of factors and fully competitive market, the wage variation arising from the long-term endogenous evolution, leads to inversely proportional relationship between the demand for labor in the urban and rural sectors, which is conducive to the transfer of rural labor force. Based on microeconomic survey data of labor flow in urban-rural coordination experimental zones in Chongqing City, this paper makes an empirical study of the main factors having a short-term impact on the labor transfer, and the results show that education level and the opportunity to participate in the training are important factors.