In this study, we evaluated the potential for exogenous thymol to slow this decline by measuring the effects of thymol application on cell wall, energy, and membrane lipid metabolism. The results showed that thymol application improved the preservation of the total soluble solids, titratable acidity, decay rate, and anthocyanin content, and effectively inhibited the accumulation of O2·-, H2O2, and malondialdehyde in blueberries during storage. Thymol application also effectively maintained fruit firmness, cell wall structure, and energy levels, while delaying the degradation of membrane phospholipids and unsaturated fatty acids during the storage of post-harvest blueberries. Therefore, exogenous thymol can maintain the quality of blueberry fruits by regulating energy and membrane lipid metabolism and reducing cell wall degradation. Thus, thymol-treatment could be a suitable biocontrol agent for maintaining blueberry quality and extending blueberry fruit storage life.