The work aims to study the effects of vacuum freeze-drying on corn seeds. The effects of vacuum freeze-drying conditions (freezing end temperature, sublimation drying temperature and parse drying temperature) on the microstructure of corn seed cells were investigated based on the optical microscope imaging and vacuum freeze-drying techniques. The variation pattern of cell morphological parameters (equivalent diameter, perimeter, area and roundness) and moisture content were compared and analyzed. A mathematical fitting model was established for the correlation between the change rate of cell morphology parameters and vacuum freeze-drying conditions. The change rate of cell morphological parameters and moisture content were negatively correlated with the freezing end temperature. With the increase of sublimation drying and parse drying temperature, the change rate of cell morphological parameters and moisture content tended to decrease and then increase. The sublimation drying temperature had the greatest impact on the change rate of morphological parameters of corn seeds. The moisture content is the lowest (12.81%) at the final freezing temperature of −25 ℃, sublimation drying temperature of 5 ℃ and parse temperature of 40 ℃. The cells have the smallest rate of change in equivalent diameter (9.2%), perimeter (8.4%), area (17.68%) and the roundness (1.78%) is less than 4%, indicating the best drying results. By the quadratic polynomial model, the coefficient of determination R2 is closed to 1 and FSSE and FRMSE are closed to 0. This mathematical model can effectively describe the effects of various vacuum freeze-drying conditions on the morphological parameters of corn seed cells and control the quality of corn seed after vacuum freeze-drying within a certain range