Because of their thin and fragile peels, harvested wax apples are perishable and prone to chilling injury when stored at low temperatures, resulting in their short shelf life. In this study, to investigate the physiological and quality changes that occur to wax apples during their storage and establish suitable controlled atmosphere (CA) storage conditions, we explored the application of CA storage technology in storing “Pink” wax apples at 1%, 3%, and 5% O2. The results indicated that storage at 1% O2 resulted in an odor in the wax apples, hence affecting their taste. Storage at 1%, 3%, and 5% O2 considerably decreased the rate of chilling injury to the apples at 10 °C and delayed electrolyte leakage from the peels. Moreover, storage at 3% O2 + 1% CO2 or 5% O2 + 1% CO2 helped preserve the total phenolic and anthocyanin content in the pulp during the storage period and delayed electrolyte leakage and chilling injury in the peels, thereby increasing the fruits’ salability following 28-day storage. Therefore, to achieve long-term storage of “Pink” wax apples, a temperature of 10 °C with 3%–5% O2 + 1% CO2 are considered favorable storage conditions.