The operation mechanism of the three level bidirectional closed loop operation network is analyzed. Then, the problem is formulated as a mathematical programming model with the objective function of minimizing cost. Because of the problem belonging to the NP problem, the traditional cutting plane method(MIP-CPM) for solving the mix integer programming model is not efficient to be used. Therefore, the improved genetic algorithm with three segment coding(IGA-3SC) strategy is presented. The three segment coding strategy is provided. The initial solution generation mechanism with the value of the three segment gene site is given. The update process based on genetic operations is explored, and the IGA-3SC solution strategy is finally obtained. The simulation experiments on different scales are used to study the two methods. The numerical simulation results show that the overall performance of the IGA-3SC strategy is better than the traditional MIP-CPM method. The IGA-3SC solution method can get higher quality solution than the MIP-CPM solution method. The computing speed of the IGA-3SC solution strategy is also better performance than that of the MIP-CPM method.