Air-based precooling methods including room cooling and forced-air cooling were traditionally used for postharvest horticultural products. In this study, disturbed-air cooling with different layouts was proposed for the trade-off between room cooling with long cooling time and forced-air cooling with high energy consumption. Lab-scale experiments with 30 bins of postharvest apples were conducted using the aforementioned methods to measure the temperature history. Multiscale thermodynamic analyses from energy, entropy, exergy, and entransy perspectives were then performed. The time evolution of transient quantities and overall comparison of the trade-off performances were further discussed. The ventilation power and transformed heat became more significant respectively for the total energy consumption and heat load during the precooling processes. The rates of entropy generation, exergy destruction, and entransy dissipation reduced in consistent with the tendency of heat rejection from all bins. The major part of these losses was resulted by the ventilation for convective heat transfer between cold air and apples and became more significant during later stage of precooling processes. The middle-parallel disturbed-air cooling achieved the best trade-off between the lowest energy consumption for room cooling and the lowest maximum seven-eighths cooling time for forced-air cooling by respectively reaching 81.68% and 28.82% of the optimization potential. The best trade-off between the lowest thermodynamic loss for room cooling and the lowest heat transfer ability loss for forced-air cooling was also achieved by this method with around 55% to 62% optimization of the coefficients of performance, around 83% optimization of the entropy generation ratio, around 58% to 62% optimization of the exergy destruction ratio, and around 36% optimization of the entransy dissipation ratio.