Korean melon (K-melon, Cucumis melo L. var. makuwa) is a key horticultural crop in the Republic of Korea, but its short shelf life restricts long-distance export. This study evaluated the modified atmosphere (MA) films of varying oxygen transmission rates (OTR) at controlled atmosphere (CA) storage under real maritime export conditions to Vietnam. In the non-permeable OTR 0 (Control) treatment, internal O₂ rapidly declined below the anaerobic compensation point (1.67% at 10d and 0.47% at 10+3d) while CO₂ accumulated to 32–36%. This ultra-low oxygen environment induced anaerobic metabolism, evidenced by strong accumulation of fermentative metabolites such as lactic acid, acetoin, and 2,3-butanediol, along with glucose/fructose retention and increases in alanine and γ-Aminobutanoic acid (GABA). These changes disrupted glycolysis and the Tricarboxylic acid cycle (TCA), consistent with CA shock, and were accompanied by rind blackening, elevated weight loss, and hue angle shifts toward yellow-orange. By contrast, OTR 10,000 and OTR 30,000 films significantly suppressed weight loss and color changes. Partial least squares-discriminant analysis (PLS-DA) identified volatile organic compounds, namely acetoin, 2,3-butanediol, and hexanal, as key discriminant metabolites, with OTR 30,000 clearly separated from other treatments at 10+3d, indicating minimal fermentation and oxidative stress. Microbial assays revealed a dose-dependent reduction in bacterial counts with increasing OTR, while fungal growth was most strongly suppressed under OTR 10,000. Overall, OTR 30,000 maintained the lowest and most stable levels of stress-related metabolites, minimized microbial proliferation, and preserved metabolic stability throughout shipping. This study provides the first quantitative evidence of anaerobic metabolic transition and primary metabolite accumulation in K-melons under actual export trials. The findings demonstrate that optimizing MA film permeability, particularly OTR 30,000 films, offers a practical and cost-efficient strategy to extend shelf life, maintain quality stability, and enhance the global export potential of K-melons.