In this paper, we propose a new freight mode to describe how the designed HSR freight train serve for express delivery. We introduce the functions of the hubs and design the hybrid hub-and-spoke network of road-rail intermodal transportation from the perspective of planners, which features as single allocation rule and configures varying levels of hubs. The problem is accurately described by a mixed integer programming model with the objective to minimize total construction cost and total operation cost. We develop a hybrid heuristic algorithm based on a greedy strategy to obtain the levels of hubs, customer allocation and cargo routing. Taking the example of HSR freight network consisting of 50 cities in China, numerical experiments are conducted on the basis of forecasting data from the real-life express market to obtain the hub location schemes. The validity of the model and the performance of the algorithm are verified.