•Numerical modeling of an integrated refrigerated container.•Different cargo pallet arrangements and cargo packaging boxes are tested.•Airflow short-circuiting has both positive and negative effects on cargo cooling.•Improving vertical airflow in cargo pallets enhances cargo cooling than air gaps. Improving the performance of a refrigerated container is crucial in effectively preserving thermal-sensitive cargo. The combined effect of vertical airflow resistance and airflow short-circuiting in air gaps play a vital role in cargo cooling. This study numerically investigates the effects of cargo vertical airflow resistance and air gaps between cargo pallets using two commonly used apple packaging boxes, each stacked in six different cargo pallet arrangements. A heat transfer enhanced refrigerated container design and a numerical model developed from the present authors’ previous studies are used. The numerical model uses the porous medium model to incorporate the refrigeration unit and cargo within the refrigerated container. Additionally, the numerical domain includes the T-bar floor in the refrigerated container. Initially, the airflow characteristics based on vertical airflow resistance and air gaps are discussed. Then, the corresponding effects on cargo cooling are addressed. Results show that the air gaps between the cargo pallets have positive and negative effects on cargo cooling. In cargos with lower vertical airflow resistance, an increase in air gaps leads to reduced cargo cooling and elevated temperature non-uniformity. Conversely, cargos with higher vertical airflow resistance experience increased cooling rates and reduced temperature non-uniformity with the increase in air gaps. However, avoiding airflow short-circuiting through the air gaps between the cargo pallets and improving the vertical airflow inside the cargo pallets can provide better cargo cooling, which outweighs the positive cooling effect of the air gap.