The work aims to expound the ventilation mechanism of microporous film for fruit and vegetable packaging and established a relevant theoretical ventilation model to guide the design of modified atmosphere packaging (opening scheme) for fruits and vegetables. The diffusion mechanism of gas molecules in the gaps of microporous and polymeric films was analyzed by thermodynamics and gas molecular dynamics theory, and a theoretical model of permeability of microporous films was established on this basis. The validity of the theoretical model was verified by detecting and analyzing the change of O2 concentration in the microporous packaging bag. The results of the cherry rot rate test showed that the model was helpful for cherry storage. The measured O2 concentration in the microporous bag designed according to the theoretical model was very close to the preset concentration, and the cherry decay rate in the bag was the lowest. In conclusion, the theoretical model can well characterize the diffusion mechanism of O2 molecules in microporous membranes, and the designed microporous gas packaging can effectively extend the shelf life of fruits and vegetables.