The purpose of this study is to explore the possibility of applying research collaboration as a new way of measuring research performance in Korean universities. In this study, we examine whether the activeness of research collaboration between university---government---industry can also enact as a way to measure the research performance aside from the typical indicators such as number of published articles or citations resulted from universities. Also this study focuses to analyze whether such performance differs according to universities' characteristics and disciplines. For the analysis of the study, we gathered publication and citation data (2000---2009) of 46 Korean universities that are actively involved in research and analyzed their science citation index-expanded and the social sciences citation index (SSCI) data. Notable findings include (1) Several low ranked universities have shown rapid improvement with their research performance despite the rigid hierarchical characteristic of Korean higher education system, (2) Although universities in Korea are involved in various kinds of collaboration methods, it was evident that such dynamic is not necessarily reflected in existing hierarchy structure, (3) Academic relations with education oriented universities and research oriented universities have different dynamics and patterns in research collaboration, (4) In terms of the collaborative publication rate, private universities collaborate more actively amongst university sector whereas public universities collaborate more with government and industry. (5) Due to the nature of the social science subject itself, it was found that the research in SSCI is inevitably more based on the researcher's independence, hence more international collaboration was found amongst researchers in natural science and engineering subjects.