Aquatic products are a high-quality source of protein for humans, and the changes in protein during aquatic product processing are crucial for nutritional value, product performance, and consumer health. With the advancement of science and technology, aquatic product processing methods have become increasingly diverse. In addition to traditional methods such as thermal processing (steaming, roasting, and frying) and pickling, emerging non-thermal processing technologies, such as high pressure, ultrasound, and irradiation, are also being applied. During (ultra-)processing, aquatic products undergo complex biochemical reactions, among which protein oxidation significantly affects the quality of aquatic products. Protein oxidation can alter the molecular structure of proteins, thereby changing their functional properties and ultimately impacting product quality. This paper primarily explored the effects of protein changes under different processing methods on aquatic product quality and human health, as well as techniques for controlling protein oxidation. It aims to provide a theoretical basis for selecting appropriate processing methods, improving aquatic product quality, and controlling protein oxidation in aquatic products, and to offer scientific guidance for practical production.