Harmful subsidies awarded by states facilitate illegal, unreported, and unregulated (IUU) fishing, which causes negative impacts on ocean ecosystems, seafood value chains, society, and global food security. The World Trade Organization Agreement on Fisheries Subsidies, adopted on June 17, 2022, aims to improve global fishery governance through trade measures and is regarded as a major step toward the achievement of the United Nations 2030 Sustainable Development Goals. The objective of this study is to offer a better insight into the interpretation and future implementation of the WTO Agreement on Fisheries Subsidies. Based on the status quo of international and regional fishery governance legal systems and management regimes in the regulation of IUU fishing, this study reviews the legislative process of the WTO Agreement on Fisheries Subsidies, analyzes five main controversial issues, and explores the conflicts of interests of different countries during the discussion. In the future, states should promote the transformation of the fisheries sector by reducing harmful subsidies for IUU fishing and enhancing cooperation among coastal states, flag states, port states and relevant RFMOs.