The Korean fisheries industry is a traditional business, the majority of which are small and medium-sized enterprises (SMEs). It has played an important role in the South Korean economies in the past several decades, but it currently faces the limitations of growth potential and profitability due to declining workforce, aging populations, deteriorating fishery environments, climate changes, and rapid changes in the global industrial ecosystem. Many studies have suggested solutions for the fisheries industry in macro perspective, but there are rarely any studies taking the strategic approaches for the problem. If it is possible for governments to support the companies that are likely to increase their value-added selectively, it will break through the current situation more effectively. This paper introduces a study on the selection method utilizing data envelopment analysis (DEA) to find SMEs with potentials to increase profits and growth. We suggest selecting SMEs with high management efficiency and ability to utilize intangible assets as the target companies. We also suggest policy objectives for SMEs in the domestic fisheries industry based on the results of DEA analysis and propose a data-based method for the policy decisions.