The Belt and Road Initiative (BRI) entails investments to improve overland (rail) transport between Europe and China. This paper introduces a microscopic Multi-Commodity Flow Service Selection Problem for freight transport under the BRI and provides a decision tool for shippers to make door-to-door service plans. The minimizing objective function considers transportation costs, in-transit inventory costs, and carbon emissions. A series of sampled data of each provincial region of China are collected from Chinese multimodal transport operators. Results show that inland regions are strongly attracted to the rail mode for shipments to Europe. However, the “last mile” (including “first mile”) transport from the shipper to the long-haul transport terminal strongly influences this choice, and carbon emissions are strongly influenced by the available last mile transport links. Under the dual impact of in-transit inventory and carbon emission costs, regions that prefer rail to maritime are much further east than suggested by previous literature.