The Iranian logistics industry, despite its geopolitical advantages and access to international transit routes, faces significant structural and institutional challenges in developing innovation capabilities due to uneven concentration of financial resources, weak information and technology infrastructures, and a lack of coordination mechanisms among institutions. Intermediary organizations play a key role in bridging logistical firms and actors in the innovation ecosystem—such as R&D centers, science and technology parks, and investors—thereby reducing structural gaps and strengthening the flow of knowledge and technology. This study employs a mixed qualitative–quantitative approach and multilevel network analysis to examine the performance of 47 intermediary organizations selected from 127 active entities. Data were collected through semi-structured interviews and a network questionnaire and analyzed using multivariate regression. Findings indicate that only 15% of the organizations possess a real capacity to facilitate innovation. The main barriers include limited access to financial resources, inadequate ICT infrastructure, and a lack of cross-sectoral coordination. In contrast, successful intermediaries that have reinforced their performance by developing digital platforms and creating innovative financing channels achieved an average effectiveness coefficient of 0.84. It is recommended that policymakers and industry managers enhance IT infrastructure, facilitate financial access, and improve coordination mechanisms and national support policies to strengthen intermediaries’ role in the country’s logistics innovation ecosystem.