Considering the decision-making variables of the capacities of branch roads and the optimization targets of lowering the saturation of arterial roads and the reconstruction expense of branch roads, the bi-level programming model for reconstructing the branch roads was set up. The upper level model was for determining the enlarged capacities of the branch roads, and the lower level model was for calculating the flows of road sections via the user equilibrium traffic assignment method. The genetic algorithm for solving the bi-level model was designed to obtain the reconstruction capacities of the branch roads. The results show that by the bi-level model and its algorithm, the optimum scheme of urban branch roads reconstruction can be gained, which reduces the saturation of arterial roads apparently, and alleviates traffic congestion. In the data analysis the arterial saturation decreases from 1.100 to 0.996, which verifies the micro-circulation transportation's function of urban branch road network.