We proposed an algorithm and a procedure of a multi-criterion analysis of the objects of transportation-logistics systems using the vector optimization of functionals, which provide a more complete representation of the properties of objects and processes. The algorithm is based on a statistical analysis of empirical data, analysis of the influential factors and qualitative characteristics of the processes, which makes it possible to more reasonably define the form of a quality function and to form criteria. The essence of the proposed procedure of a multi-criterion analysis is the vector optimization of functionals whose equations are introduced with the characteristics of rate of change in the examined processes. In contrast to the existing procedures that characterize a state of the system and separate elements, the given technique allows us to more fully and objectively estimate dynamic properties of the transportation and logistics processes. Using the movement of cargo flows through the customs warehouse as an example, we have shown the statement of separate mathematical models for simultaneous and independent optimization of several parameters and functionals and the formation of a complete set of effective plans for subsequent analysis by a decision-maker