This study examined conflicts involved in the merger of small schools and national universities in South Korea in terms of network structure. Using the case studies of merged small schools in the Jeonbuk and Gangwon regions and of amalgamated Kangwon-Samcheok and Chonnam-Yeosu national universities, this study applied the social network analysis(SNA) method. The analysis addressed the characteristics of conflict network structure, including sociogram, network size and centralization, and centrality. According to the analysis, first, the small schools showed the star-shaped network structure while the universities exhibited both the circular and star-shaped structure. The conflict network structure varied depending on the degree of autonomy. Second, in the case of small schools in Jeonbuk and Gangwon and of the amalgamated Kangwon-Samcheok University, the relationship conflict was found to be concentrated on specific actors, whereas the merged Chonnam-Yeosu University showed a complex conflict network structure. The study found that the more extensive and complex the conflict network, the more difficult to resolve the conflict. Third, the Ministry of Education was the key actor of conflict network for small schools, while the university leading the merger was the key actor. Primary conflict parties varied depending on the level of educational institutions.