This research developed a new integrated method for addressing the deficiencies and gaps generally found in past studies on benchmarking and for benchmarking intellectual capital (IC) in the underdeveloped domain of logistics. To resolve the lack of consideration of relationships among past benchmarking concepts and the impacts of their managerial factors, as well as to examine the wide range of elements and indicators of IC influencing the sustainable development of organizations, the proposed approach integrated the analytic network process and the concept of thinking and non-thinking assets with the generic benchmarking procedure. This new hybrid method was implemented in four commercial companies in courier service. The proposed method prioritized and identified the magnitudes of the factors focused upon, including the IC elements, and their performance measures by considering the fundamental characteristics of intangible assets. The obtained results highlight that management focuses on the IC of the best performer and other companies. This benchmarked outcome showed gaps and improvement as well as sustainable development opportunities for inferior logistics companies. The improved framework provides more systematic and specific benchmarking processes to consider, obtain, and compare the in-depth details of IC management. Moreover, ours is the first research on benchmarking that specifically focused on IC management in logistics service providers.