TBO operation is the mainstream direction of the future civil aviation control operation, to alleviate the current air route intersection flow and reduce congestion. In the background of TBO operation, the dimension reduction method to build the font configuration was used. The model of route crossing point was established, and the capacity formula of single route crossing point and shaft configuration crossing point was proposed. Combined with the simulation of a civil aviation route crossing point in peak time, the results showed that the shaft configuration capacity increased by 35.4% compared with that of single route crossing point. Then, the objective function of the model was set, and the genetic algorithm was used to solve the model. It is concluded that compared with the single route crossing point, the cross point of the I-shape configuration reduces the cost of flight delay by 49% and the average delay time of passengers by 52.7%. The results show that, for high-flow route intersections, congestion can be effectively alleviated and route resources can be coordinated by changing the well shape configuration.