Aquaculture relies heavily on formulated feed, with feed costs accounting for approximately 50% of the total production expenses. High-protein feed is expensive, and some raw materials are dependent on imports. Organic waste, primarily from food scraps and agricultural residues, can be considered feed ingredients to reduce costs. Through fermentation, the nutritional value of these feeds can be enhanced, promoting the growth of aquatic animals, such as fish, and reducing overall costs. Enzymatic hydrolysis and microbial fermentation are commonly used bioprocessing methods, particularly suitable for unconventional feed sources. These methods not only enhance the nutritional value of the feed but also reduce the content of anti-nutritional factors, improving feed digestibility. Enzymatic hydrolysis is often combined with microbial fermentation to produce more efficient novel biofeeds. This synergistic approach enhances microbial fermentation efficiency and the degradation of macromolecules, further improving the nutritional value of the feed, promoting intestinal digestion and absorption, and enhancing animal production performance. Compared to treatments with single strains or enzymes, the synergistic fermentation of feed with microorganisms and enzymes shows more significant effects. This review summarizes the fermentation mechanisms and classifications of enzymatic hydrolysis and microbial fermentation in producing novel biofeeds. It also outlines the advantages of this synergistic process and its progress in aquatic animal production, providing a scientific basis for its broader application in aquaculture.