With the constant growth of R&D investment by government-funded research institutes, it has been increasingly necessary to evaluate the effectiveness of R&D performance. There are many approaches that have focused on R&D performance evaluation. Literature is unclear, however, how stakeholders can exploit performance results to improve their R&D capability. In this study, based on the intellectual capital possessed by research institutes, we proposed a new method to search improvement directions in R&D operation levels. To this end, formal concept analysis, which recognizes a research institution as an object, defining the intellectual capital as an attribute, was conducted. The proposed method conceptually clusters the relationship between objects and attributes and examines their hierarchical relationships. The case study shows the proposed method not only provides guidelines for improvement paths for individual research institutes but also identifies the components of intellectual capital that are meaningful in common.