Apples are preserved in cold storage within standard size crates to avoid injury during handling and are stacked in a specific manner to promote adequate air circulation. This research builds an air flow and heat transfer model of a cold room (5.75 m × 3.83 m × 3.75 m) with apple filled crates (0.55 m × 0.37 m × 0.3 m) modeled as a porous media and uses CFD simulation to study how alternate stacking impacts airflow distribution and product temperature. The conventional arrangement of crates, termed CS1, was simulated, and the resulting temperature distribution data were used to validate the model with published experimental data, a root mean square error of 1.13 °C indicates good match. The model is extended to examine temperature distribution for two additional arrangements of crates (CS2 and CS3) with changed orientations and spacing, in accordance with a specific strategy. CS3, featuring larger spacing along the z-direction, showed higher average air velocity compared to CS2 and CS1 by 7.4% and 3.7% respectively. CS3 also improved cooling rate by 25.2% and increased the number of chilled crates by 20% within 40 h, along with a reduced temperature heterogeneity (3.59 °C). The model could predict hot spots in various stacking configurations, aiding in optimal arrangement.