Crossing waypoints location problem (CWLP) is a core of air route network planning. Based on the situation, a model of multi-objective optimization for CWLP is built, judged by the two factors of total airline cost and total flight conflict coefficient and proceed from the economic and safe aspects of air route network. During the solution, multi-objective bat algorithm based on dynamic gradient weight coefficient is adopted to make sure that the cost and flight conflict coefficient can obtain optimal solutions at the same time. In the end, this paper takes Beijing flight information area as a simulation and gains four kinds of non-dominated solution by comparing BA with other algorithms. The result indicates that the BA in solving the problem can get a more optimal solution. Meanwhile, in consideration of two groups of weight according to the preference of economy or the safety, the data show that the proportional reductions of the network operation cost and conflict coefficient in these two situations respectively are 9.99%, 15.64% and -3.97%, and 65.81%, compared with the initial network. The conclusion of the simulation is that the method can provide various solutions for the decision makers in the design for crossing waypoints location.