The promising future of natural colors in the food industry aligns with the shift in consumer preference toward healthier food options. These naturally derived ingredients gradually replace their artificial counterparts and find applications in a wide range of food categories, and aquatic products have emerged as one of them. In this work, we introduced the characteristics and extraction of several main types of natural pigments and also explored the positive outcomes of integrating the pigments, such as carotenoids, curcumin, anthocyanins, and betalains, in aquatic product processing and preservation. Their outstanding antioxidant and dyeing properties contribute to the production and storage of various aquatic products. This review aims to provide a comprehensive understanding of the current state of natural pigment applications in aquatic products and to provide inspiration for future research and industry practices.