When solving a Multi-Criteria Decision-Making problem of any degree of complexity, many researchers rely on the analytic hierarchy process (AHP). To consider mutual connections between criteria and clusters at the same level and not only the hierarchical structure between criteria and subcriteria, researchers often upgrade from AHP to the Analytic Network Process (ANP), which also examines the interdependency of criteria. However, the ANP method requires a large number of pairwise comparisons. In the case of a complex decision-making problem, the authors of this paper suggest upgrading the AHP method with the graph theory and matrix approach (GTMA) for several reasons: (1) The new method is based on digraphs and permanent value computation, which does not require a hypothesis about interdependency; (2) in case of similar alternatives, the distinguishable coefficient of the new method is higher than those computed for AHP and ANP; (3) the new method allows decision makers to rank comparable alternatives and to combine structurally similar methods without increasing the number of comparisons and the understanding of the results. The developed method (AH-GTMA) is validated by a numerical example of a complex decision-making problem based on a symmetrical set of similar alternatives, a third party logistic provider (3PLP) selection problem.