Given the challenges of resource shortages, nutritional deficiencies, and environmental pollution from traditional feeds, functional formulated feeds are increasingly vital for the healthy and sustainable development of aquaculture. Microalgae are commonly utilized in aquaculture feeds due to their diverse array of natural pigments, such as carotenoids, phycobiliproteins, and chlorophylls. This chapter focuses on the “pigment intake–physiological metabolism–quality formation” framework, emphasizing the connection between aquaculture and processing. Initially, the physiological metabolism and coloring properties of dietary microalgae pigments in aquaculture are discussed. Next, from a food raw materials science perspective, the role of dietary microalgal pigments in improving the nutritional quality of aquatic products has been investigated and analyzed. Finally, the enhancement effect of dietary microalgal pigments on the flavor quality of aquatic products is explored and discussed, focusing on their unique sensory attributes, including umami, sweetness, and aroma. Future research directions will emphasize multidisciplinary collaborative innovations regarding how dietary microalgal pigments regulate physiological metabolism and improve edible quality, ultimately supporting a new fishery development model centered on “aquaculture for processing”.