ABSTRACT As fundamental components of metabolic networks, metabolites act as both energy carriers and signaling molecules, orchestrating a wide range of physiological functions. Consequently, the abundance of metabolites within tissues and cells is typically under tight regulation, with any perturbation of this metabolic equilibrium frequently triggering diverse stress responses and diseases. Recent studies demonstrated that nutritional, environmental, and pathogenic stimuli factors during aquaculture may lead to the remodeling of the fatty acid oxidation pathway in aquatic animals, altering the abundance of fatty acid oxidation‐related metabolites and subsequently triggering stress response cascades. Thus, elucidating the functional roles and regulatory mechanisms of these metabolites is critical for developing targeted strategies to mitigate these stress responses. However, the current progress of research on metabolites related to fatty acid oxidation in aquatic animals is not well summarized. Therefore, in this study, we characterize the fundamental pathways of fatty acid oxidation in aquatic animals and summarize the mechanisms by which these metabolic pathways respond to diverse aquaculture‐related stressors. Furthermore, we systematically elucidate the mechanisms through which these metabolites mediate their regulatory functions, highlighting the distinct physiological roles of the key metabolites. Additionally, we provide our perspectives on the potential applications and future research priorities of fatty acid oxidation‐related metabolites in aquaculture. This review contributes to a better understanding of the dynamics and functions of fatty acid oxidation‐related metabolites in aquatic animals and will facilitate the development of metabolites‐based therapeutic strategies, thereby increasing the sustainability of aquaculture.