Due to the decrease in coastal productivity and deterioration in the quality of ecosystem which result from the excessive overfishing of fisheries resources and the environmental pollution, fisheries resources in the Korean waters hit the dangerous level in respect of quantity and quality. In order to manage sustainable and effective fisheries resources, it is necessary to suggest the potential yield (PY) for clarifying available fisheries resources in the Korean waters. So far, however, there have been few studies on the estimation methods for PY in Korea. In addition, there have been no studies on the comparative analysis of the estimation methods and the substantial estimation methods for PY targeted for large marine ecosystem (LME) For the reasonable management of fisheries resources, it is necessary to conduct a comprehensive study on the estimation methods for the PY which combines population dynamics and ecosystem dynamics. To reflect the research need, this study conducts a comparative analysis of estimation methods for the PY in the Korean waters of the East Sea to understand the advantages and disadvantages of each method, and suggests the estimation method which considered both population dynamics and ecosystem dynamics to supplement shortcomings of each method. In this study, the maximum entropy (ME) model of the holistic production method (HPM) is considered to be the most reasonable estimation method due to the high reliability of the estimated parameters. The results of this study are expected to be used as significant basic data to provide indicators and reference points for sustainable and reasonable management of fisheries resources.