The suggested model for determining the optimal trajectories of moving consignments that form cargo flows in transport and logistics systems (TLS) is based on a combination of dynamic systems and multi-criteria optimization methods. This approach develops a methodology for solving applied control problems in TLS. Its main result is the principle of finding the maximum, subject to the criterion preferences, based on methods for determining the set of effective plans (Pareto set). At the same time, management in TLS should form models of cargo traffic taking into account the location of transport and storage complexes within the boundaries of the system being studied or designed, as well as should provide for movement of consignments according to specified performance criteria and the most rational trajectories using analytical modeling. Analytics together with digital technologies help to consider the core sense of TLS as of a subsystem of intelligent transport systems.