Here, we aimed to study the changes in proteome of golden pompano fillets during post-mortem storage. Tandem mass tags (TMT) -labeled quantitative proteomic strategy was applied to investigate the relationships between protein changes and quality characteristics of modified atmosphere packaging (MAP) fillets during superchilling (-3 °C) storage. Scanning electron microscopy was used to show that the muscle histology microstructure of fillets was damaged to varying degrees, and low-field nuclear magnetic resonance was used to find that the immobilized water and free water in the muscle of fillets changed significantly. Total sulfhydryl content, TCA-soluble peptides and Ca2+-ATPase activity also showed that the fillet protein had a deterioration by oxidation and denaturation. The Fresh (FS), MAP, and air packaging (AP) groups were set. Total of 150 proteins were identified as differential abundant proteins (DAPs) in MAP/FS, while 209 DAPs were in AP/FS group. The KEGG pathway analysis indicated that most DAPs were involved in binding proteins and protein turnover. Correlation analysis found that 52 DAPs were correlated with quality traits. Among them, 8 highly correlated DAPs are expected to be used as potential quality markers for protein oxidation and water-holding capacity. These results provide a further understanding of the muscle deterioration mechanism of packaging golden pompano fillets during superchilling.