BACKGROUNDThe improper stunning methods before slaughter could cause the fish to deteriorate more quickly during cold storage. However, it is unclear that how stunning methods affect the mitochondria structure and the role of mitochondria in the oxidation in muscle‐based food.RESULTSThis study was to explore the potential mechanism of oxidation induced by different stunning methods (hit on the head, T1; gill cut, T2; immersion in ice/water slurry, T3; CO2 asphyxiated, T4; 40% CO2+30% N2+30% O2, T5) in large yellow croaker during cold storage. The results showed that T4 samples had the minimum stress response and the mitochondrial membrane potential and permeability were less damaged. Besides, the mitochondrial functional structure and peroxisome of T4 samples were less damaged compared with other samples, which was reflected in higher total superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) activities. In terms of oxidation indices, the T4 samples showed higher pH values and iron myoglobin (MMb) contents, lower total volatile basic nitrogen (TVB‐N), thiobarbituric acid reactive substances (TBARS) after 168 h cold storage, indicating that the T4 samples significantly maintained the oxidative stability of the large yellow croaker.CONCLUSIONThe CO2 asphyxiation had the least oxidative damage to large yellow croaker during cold storage, possibly because it had the least effect on mitochondrial structure, reactive oxygen species (ROS), and antioxidant enzyme activity.This article is protected by copyright. All rights reserved.