The purpose of this study was to develop a technique for designing modified atmosphere packaging (MAP) for suppressing chilling injury (CI) in cucumber fruit using a mathematical model. The respiratory quotient (RQ) changes from 0.2% to 4% of O2 at 5°C was measured to determine the critical low O2 limit and was found to be 0.5%. Next, respiration rates of cucumber fruit stored at 5°C under various O2 concentrations were measured and modelled with the Michaelis-Menten equation as a function of O2 concentration. The model provided a good prediction of the respiration rate of cucumber fruit at any O2 concentration. A mathematical model incorporating the respiration rate and gas mass transfer through film packaging was developed to estimate the optimal O2 permeance, leading to equilibration of O2 concentration in the package at the established critical low O2 limit. To verify the effect of CO2 accumulation inside the package on CI suppression, the malondialdehyde (MDA) of the fruit packed in a low-density polyethylene (LDPE) bag with and without a CO2 absorber was evaluated. The results suggested that reducing CO2 in the package is effective for suppressing CI. Further study such as optimal design for the active MAP with a CO2 absorbent is needed to realize the maximum performance of MAP in alleviating CI in cucumber fruit.