A tandem mass tagging-labeled proteomic approach was employed to explore the relationship between quality parameters and protein changes in large yellow croaker fillets refrigerated under carbon dioxide, oxygen, and nitrogen atmospheres. After 96 h, fillets stored in carbon dioxide and nitrogen showed improved texture, water-holding capacity, and color, compared to those stored in oxygen. Functional analysis respectively identified 117 and 65 differentially expressed proteins in carbon dioxide and nitrogen, including key proteins such as troponin, myosin light chain, actin, and collagen types IV and XIII, that were linked to extracellular adhesion, cytoskeleton integrity, energy metabolism, and membrane functions. Carbon dioxide and nitrogen were detrimental to the growth and reproduction of aerobic microorganisms. High concentrations of carbon dioxide can inhibit microbial activity, while nitrogen preserves freshness by regulating the pressure balance within the packaging. These findings provided a theoretical basis for the optimized gas-conditioned preservation of large yellow croaker fillets.