This paper presents a potential solution to fill a gap in both research and practice that there are few interactions between transnational industry cooperation (TIC) and transnational university cooperation (TUC) in transnational innovation ecosystems. To strengthen the synergies between TIC and TUC for innovation, the first step is to match suitable industrial firms from two countries for collaboration through their common connections to transnational university/academic partnerships. Our proposed matching solution is based on the integration of social science theories and specific artificial intelligence (AI) techniques. While the insights of social sciences, e.g., innovation studies and social network theory, have potential to answer the question of why TIC and TUC should be looked at as synergetic entities with elaborated conceptualization, the method of machine learning, as one specific technic off AI, can help answer the question of how to realize that synergy. On the way towards a transdisciplinary approach to TIC and TUC synergy building, or creating transnational university-industry co-innovation networks, the paper takes an initial step by examining what the supports and gaps of existing studies on the topic are, and using the context of EU–China science, technology and innovation cooperation as a testbed. This is followed by the introduction of our proposed approach and our suggestions for future research.