In recent years, with the popularization and advancement of animal welfare concepts, the research scope has expanded from terrestrial to aquatic organisms. Related issues have garnered increasing attention from government agencies, animal protection organizations, researchers, and aquaculture practitioners. Habitat conditions, aquaculture practices, fishing methods, sales processes, and artificial stocking can potentially affect fish welfare. Based on an overview of the concepts and current progress in fish welfare research, this study summarizes the main factors affecting fish welfare. These encompass intra- and interspecific interactions, environmental conditions such as water quality, stocking density, and nutritional supply, as well as key production management measures including genetic breeding, live transport, grading, and slaughter. This study further reviews relevant evaluation indicators for fish welfare, including (1) behavioral metrics such as swimming activity, exploration, aggression, schooling, respiratory rate, feeding, stereotyped behaviors, and escape attempts; (2) physiological and biochemical parameters such as neuroendocrine regulation, oxidative stress, and immune and hematological responses; and (3) emerging and integrated assessment approaches, including methods based on cognitive bias tests and lateralization analysis, as well as other comprehensive evaluation methods and welfare assessment tools. However, the limitations of the current fish welfare research were highlighted and future work, grounded in species conservation and ethical considerations to systematically address fish welfare issues across different scenarios, was emphasized. Fully respecting the ecological habits of fish was proposed, focusing on safeguarding their natural behavioral expressions and maintaining their healthy physiological states. In addition, establishing a fish welfare advancement mechanism underpinned by policy and regulations, supported by scientific research, and aimed at public participation, to achieve coordinated development of fisheries production practices and fish welfare protection was emphasized. This study provides a theoretical basis for establishing a standardized fish welfare assessment framework and promoting welfare-oriented, healthy aquaculture practices.