‘Fuji’ apples that are commercially debagged before harvest are more resistant to external CO2 injury, a physiological disorder, than without debagging. In this study, debagged (bags removed 30 d before harvest) and bagged (bags not removed until harvest) apple fruit were stored in air and in controlled atmosphere storage regimes of 4 kPa O2/0 kPa CO2 and 4 kPa O2/5 kPa CO2 to explore the effects of preharvest debagging on the occurrence of external CO2 injury and the underlying mechanism of the injury. Debagging reduced disorder occurrence of the fruit from 8 d to at least 60 d. Preharvest debagging suppressed the accumulation of reactive oxygen species and malondialdehyde under CO2 stress by increasing the concentrations of antioxidant substances, including phenolics and ascorbic acid, and the activities of superoxide dismutase and catalase. In vitro free radicals scavenging activities further confirmed that the debagged fruit had higher antioxidant activity than the bagged fruit under elevated-CO2 storage conditions. Compared with the bagged fruit, the debagged fruit had higher contents of adenosine triphosphate (ATP) and adenosine diphosphate, level of energy charge, and activities of energy metabolism-related enzymes, including succinate dehydrogenase, cytochrome C oxidase, and Ca2+-ATPase under CO2 stress. ATP treatment inhibited the disorder occurrence ‘Fuji’ apple. These results reveal that the effect of preharvest debagging on inhibiting the occurrence of external CO2 injury of ‘Fuji’ apple was associated with the improvement of antioxidant capacity and energy status of apple peels under CO2 stress.