This study aims to analyze the income structure, cost structure, and profit structure based on data related to the business performance of the boat seine fishery from 1990 to 2020, and to identify the direct and indirect factors affecting fishery profitability through panel regression analysis. The main analysis results are as follows. First, it was found that fish catch has a significant amount of impact on fishery profitability, which is a key factor in improving the profitability of anchovy boat seine fishery. Second, it is necessary to develop carbon-reduced fishing gear, develop fleet-reduced fishing gear, and improve the operating system in order to increase fishery profitability for the short run. Third, it is necessary to create and maintain sustainable profitability for the long run, the continuous fishing vessels buyback program, an active responses to climate change, and the follow-up investigations about marine aggregate extraction in the south sea EEZ are needed.