The production of aquatic products is always increasing worldwide, due to their high nutritional value. However, a large number of by-products are produced during the consumption and processing of aquatic products, causing serious resources waste and environmental pollution. On this basis, the by-products of aquatic products were developed and applied in many fields according to their different characteristics. Among them, the by-product proteins have been widely recycled and utilized in practice due to its unique functions and high added value. Therefore, this article reviewed the typically physical, chemical and biological methods for recycling the proteins from aquatic products. Meanwhile, we also introduced the research progress in the high-value utilization of by-product proteins from fish, crustaceans and shellfish, as well as their future development trend, with the purpose of further enhancing the comprehensive utilization of aquatic by-products and promoting the high-quality development of aquatic product industry. Generally, the aquatic products from fishing or aquaculture often needed to be processed before their marketing. However, massive by-products were left after being processed, and they must undergo further treatment to obtain end-products with high added value. Among these by-products, proteins accounted for a large proportion and had higher nutritional value. The efficiency of traditional technology to recycle by-products of different aquatic products was limited, and the yield was very low, therefore, it was difficult to potently recycle a large number of by-product proteins from aquatic products. In the past century, the scientists in academic and industrial community made great efforts to fully recycle the by-product proteins of aquatic products, and achieved many end-products through physical, chemical and biological methods. With the advance and innovation of science and technology, the recycling conditions of by-product proteins from aquatic products have been greatly optimized, and the recyclable types of by-products have greatly expanded, as well as the proteins yield has been significantly improved. Therefore, the research hotspots of by-product proteins from aquatic products mainly focused on two aspects: innovative recycling methods and enhancing the added value of utilization. With the continuous development of molecular biology and polymer science, the researchers could modify the by-product proteins from aquatic products through physical, chemical and biological methods, which could not only improve and enhance their biological properties, but also broaden the applications of related products range. China's aquaculture output has ranked first in the world for 28 consecutive years. However, the research on the high-value utilization and industrial application of aquatic by-products needed to be further improved. Moreover, from the perspective of industrial development, whether it was the introduction and development of by-product development technology, or the formulation and management of related product standards, China is facing many practical problems and challenges. Consequently, it is necessary to focus on the current situation and development trend, carry out the next step of planning, which will introduce new vitality to the aquatic product processing industry. In the future, the commercial development of by-product proteins from aquatic products will bring more possibilities and development prospects. More and more foods and drugs prepared using by-product proteins will be approved and promoted, which will provide a driving force for the further development of aquatic products industry.