Fruit bagging has been used commonly in commercial orchards in recent years in China. The bag acts as a barrier to protect fruits from injury or damage of external causes. Bagging of fruits on the tree provides an effective alternative to improve the quality and safety of fruits, and probably is one of the best methods of growing organic fruits for commercial growers. Some studies had verified that the appearance of bagged apple fruits was better than that of non-bagged fruits. The microenvironments inside the bags and the effects those microenvironments had on the structure of the apple peels were studied in our experiments to explain why bagged apple fruit develop beautiful appearance. In the experiments, apple fruits (Malus domestica Borkh. cv.'Fuji’) were bagged with two-layer paper in mid June (about 45 days after petal fall) and remained bagged until 4 weeks before harvest. Non-bagged fruits acted as the control. The photosynthesis in the bagged fruit peels was inhibited by the dark microenvironment created by the bag. Inside bag temperature and humidity were higher like mini-greenhouse. The transpiration rate that may results in cuticle crack of apple peel was decreased by the higher relative humidity. Protected by bag, the fruits were avoided the physiology disorders by direct sunlight, avoided the attack by summer insect pests and diseases, and avoided the pollution of pesticide sprays, so the fruit surface was cleaner and glossier, and scattered with less and lighter-color lenticel pits. Observed by transmission electronic microscope, the ultrastructures of the fruit first layer cells were less dense deposits in bagged fruit compared with that in control fruit. In the cytoplasmic matrix of bagged fruit peels, lipoplast globules were dissociated, but integrated lipoplasts were scattered in that of control fruit peel. The results indicated that bagging reduced the accumulation of materials that form the cuticle in peel cells. Protected by bag, the cuticles of the fruits' surfaces were thinned and developed uniform and shallow cracks (observed under KYKY-2800B scanning electronic microscope) by the uniform surface temperature and high relative humidity. The density of cracks increased after bag removal for direct exposure to sunlight and lower air relative humidity. These results provide a mechanism underlying the effects of the bag microenvironments on fruit quality, and support the use of calcium supplementation in fruits after bag removal.