Animal toxins present an enormous threat to global health, necessitating urgent attention to their management and research. Mitochondria have been identified as a key focus in understanding the pathophysiology and clinical applications of animal toxins. This review provides a comprehensive analysis of the relationship between mitochondria and animal toxins from multiple dimensions, aiming to promote the toxicological research on animal toxins, investigate and evaluate their potential clinical applications, and identify novel drug targets for the development of new antitoxin drugs.