In current literature and practices, there are no systematic and user-oriented intermodal transportation performance measures. After identifying customer needs and transportation goals, this paper proposes a set of system-level performance measures for intermodal transportation that are user-oriented, scalable, systematic, and scientific. The measures can be used to compare intermodal design alternatives or to evaluate existing transportation systems with any size and any mode. The highway system in Mississippi is analyzed as a case study. The case study demonstrates the existing data sources, the methods of calculating the measures, and the means of evaluating transportation systems with the measures.