Prepared aquatic foods refer to ready to eat, heat, cook, and use aquatic products. These foods are gaining popularity as a result of consumer preference for their peculiar flavor. Flavor deterioration of prepared aquatic foods directly impacts the sensory quality and consumer acceptance. Identifying the mechanisms involved in flavor development and offering strategies to regulate flavor are crucial, as the flavor of prepared aquatic foods alters under various processing and storage conditions. Microorganisms play a crucial role in flavor evolution by participating in biochemical metabolic reactions and regulating quorum sensing systems. In this review, microbial species associated with the flavor of prepared aquatic foods are summarized. The mechanisms of protein, lipid, and carbohydrate metabolism, as well as quorum sensing mediated by microorganisms in the flavor evolution of prepared aquatic foods, are also reviewed. The regulation of quorum sensing, non-thermal sterilization, antibacterial packaging, artificial intelligence colony prediction, and flavor-targeted compensation for flavor control are also discussed with current and prospective views. This review aims to provide insights into the promotion of desired flavor compounds and control of off-flavor substances in prepared aquatic foods from the perspective of metabolic mechanisms and quorum sensing in microorganisms.