Collagen is an essential macromolecular protein in animals and the extracellular protein involved in the mechanical protection of animal tissues and organs. As the focus of attention in the collagen industry in recent years, the shortcomings of traditional protein extraction methods in terms of extraction rate and environmental protection are gradually emerging. In this review, the effects of molecule composition, types, sources, and pretreatment methods on collagen extraction processes are summarized. The effects of raw materials, traditional extraction processes (acids, bases, enzymes) on collagen yield and function are compared. The current status of aquatic collagen applications in food quality, food preservation, pharmaceuticals and the industrial feasibility of new collagen extraction methods (subcritical water, supercritical fluid extraction) are analysed. The aim of this study is to provide theoretical support for the high value utilisation of aquatic resources by proposing a "physical/biological-acid-composite enzyme" process optimisation scheme for aquatic collagen, which has a low protein extraction efficiency and a high impact on the structure of raw materials.