We explore a freight routing problem wherein the aim is to assign optimal routes to move commodities through a multimodal transportation network. This problem belongs to the operational level of service network planning. The following formulation characteristics will be comprehensively considered: (1) multicommodity flow routing; (2) a capacitated multimodal transportation network with schedule-based rail services and time-flexible road services; (3) carbon dioxide emissions consideration; and (4) a generalized costs optimum oriented to customer demands. The specific planning of freight routing is thus defined as a capacitated time-sensitive multicommodity multimodal generalized shortest path problem. To solve this problem systematically, we first establish a node-arc-based mixed integer nonlinear programming model that combines the above formulation characteristics in a comprehensive manner. Then, we develop a linearization method to transform the proposed model into a linear one. Finally, a computational experiment from the Chinese inland container export business is presented to demonstrate the feasibility of the model and linearization method. The computational results indicate that implementing the proposed model and linearization method in the mathematical programming software Lingo can effectively solve the large-scale practical multicommodity multimodal transportation routing problem.