This study focuses on the green economic growth of marine fisheries and explores the relationship among environmental regulations (ERs), industrial structure (INS), and the green total factor productivity of marine fisheries (MGTFP). Against the backdrop of global climate change and increasing pressure on resources and the environment, a green fisheries economy has become key to achieving sustainable development. This study selects panel data from 11 coastal provinces and municipalities in China spanning from 2014 to 2023 and, through quantitative analysis, evaluates the implementation effects of ER policies on marine fisheries’ production methods, INS, and MGTFP. When measuring the MGTFP, this study innovatively incorporates fishery disaster economic losses as an undesirable output and employs the super-efficiency SBM-GML model for precise calculation. The results of the study showed that ERs was able to promote the increase in MGTFP, and the effect of REC was stronger. The mediating effect model suggests that industry structure mediates this process. The results of threshold effect analysis show that both ERC and ERM exhibit significant single-threshold effects. This study aims to provide empirical support and policy recommendations for the government to formulate more effective environmental protection policies and promote the transformation and upgrading of the marine fisheries sector, thereby fostering the green development of China’s marine fisheries.