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A new working mode of overloaded traffic control for rural highways is presented, and a location-routing model is built to optimize the check base distribution and the control vehicles’ routing schemes. Then, for the location-routing model with a large set of location alternatives and an unknown settable number of check bases, a multiple ant colony optimization algorithm is designed to solve the model. Furthermore, actual data from Guiyang rural highways are used to perform a numerical analysis. The results indicate that the model can be used to obtain the optimal base location-vehicle routing scheme to verify the feasibility of the model and the algorithm. The model and algorithm can help managers to make decisions on locating the check bases and routing the control vehicles.