An important reason for the long-term existence of large-scale informal emigration of Chinese population is household register system which separates the urban and rural areas. From the perspective of economics, the household register system reform difference in the reform degree and progress between the governments of the cities with different grades has endogenous cause, the results derived from quantitative model show that under the condition that other prerequisites do not change, the original motive power of agricultural labor flow comes from the combined decision with urban and rural utility maximization, that the scale of non-agricultural employment transfer from agricultural labor is endogenously regulated by the household register system threshold with urban and rural two dimensions and by the difference in income and welfare based on the difference in the household register status and meanwhile the deployment of the household register between different cities for the non-agricultural employment of transferred labor and their carried population are directed by this.