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In this study, we aim to develop a system optimization model of Railway Freight Transportation Routing Design (RFTRD) and conduct solution analysis which is based on the improved multi-objective swarm intelligence algorithm. The proposed improved multi-objective swarm intelligence algorithm is applied to solve the combinatorial optimization problem of railway door-to-door freight transportation through design, and provide decision support for railway vehicle door-to-door freight transportation through design. The optimization results shows that, the random multi-neighborhood based multi-objective shuffled frog-leaping algorithm with path relinking (RMN-MOSFLA-PR) can be better applied to solve the combined multi-objective optimization problem, and this proposed improved algorithm can find Pareto frontier through the comparative analysis in the design example of railway door-to-door freight transportation. The frontier can provide support for railway transportation enterprises, arrange the decision-making of the starting and ending stations for multiple shippers, and optimize the use of existing transportation resources, so as to reduce the transportation cost and time of the system.