The satisfaction of requirements and preferences of shippers is critical to enable the practicability of solutions that are derived from intermodal transportation routing problems. This study aims to propose a decision process to help shippers participate better in routing decisions. First, we considered shippers’ requests on transportation cost, timeliness, reliability, and flexibility to construct a multi-objective optimization model. Then, to solve the interactive optimization method that was proposed, NSGA-III was applied to obtain the Pareto front and dominance-based rough set approach to model the preference information. Finally, a case study was conducted and an expert was invited as decision-maker to demonstrate the applicability of the proposed model and the effectiveness of the interactive method for shippers. The results are expected to provide shippers with more rational transportation schemes and insights for the sustainable development of intermodal transportation.