Changes in the quality of blue honeysuckle fruit following exposure to air or controlled atmospheres (CA1: 20% O2 and 20% CO2; CA2: 5% O2 and 20% CO2; CA3: 5% O2 and 10% CO2) were investigated. The 'Lanjingling’ blue honeysuckle was stored at a temperature of −1 °C for a duration of 28 d. An elevated concentration of CO2 led to a reduction in fruit weight loss, ethanol content, and respiration rate, while simultaneously increasing the epicuticular wax coverage index, firmness, TSS, ascorbic acid, polyphenols, and antioxidant capacity. Notably, treatment with high levels of carbon dioxide (20% CO2) led to an approximately 150% increase in total anthocyanin content compared to control conditions. Additionally, it was observed that reducing the oxygen content from 20% to 5% had a detrimental effect on the antioxidant capacity of blue honeysuckle during storage. Specifically, there were decreases of 10.4%, 16.8%, and 6.7% in DPPH, ABTS, and FRAP, respectively. The respiration rate is increased by treatment with 5% O2 and 5% CO2, which may result in accelerated senescence of blue honeysuckle. After 28 d, the treatment resulted in a respiration rate that was 1.49 times higher than the control. Hence, it can be deduced that maintaining a controlled atmosphere containing 20% O2 and 20% CO2 can be deemed an effective method of blue honeysuckle for prolonging storage life and safeguarding its bioactive components.