As a measure to improve the operational efficiency of the Korean supercomputer joint utilization resources, an efficiency analysis using DEA was conducted to derive the improvement level of the input and output factors of the operation plans of seven specialized centers. The factors that constitute the objective function of efficiency were identified through the operation plans submitted by the specialized centers, and DEA analyzed the improvement factors and levels of inefficient specialized centers through the CCR and BCC models, and then conducted an additional super-efficiency analysis to compare the relative efficiency levels among the efficiency groups. As a result of the analysis, the inefficiency of specialized centers in the meteorological/climate/environmental fields was identified from the reference group, and the need for improvement and the level of improvement of input and output variables were identified. In addition, the authors suggested ways to improve the establishment of resources and operational targets, such as a joint utilization ratio to secure financial efficiency at the government level in establishing a joint utilization resource.