The article presents an approach for choosing alternative transport routes in a multimodal transport system. This approach includes (1) the transportation needs hierarchy method and (2) the Evaluation of Petri Nets (E-nets) as a modeling tool. The purpose of the study is to develop a methodology for choosing alternative routes for the transportation of goods, taking into account the criteria used by decision-makers. The structure of the hierarchy of transport needs is proposed, which consists of five levels: geographical, economic, institutional/political, infrastructural, and technological. For each of the levels, sets of indicators characterizing it are proposed. The Petri net model captures system dynamics and allows the evaluation of alternative routes. A set of standard rules for transforming the structure of the hierarchy of transport needs into a Petri net is proposed, considering preference parameters for each level of the hierarchy. The proposed approach and the models built on its basis can be applied in the field of cargo transportation to improve operational efficiency and improve decision-making results.