CO₂ concentration has a significant effect on quality of cold-stored apples. High indoor CO₂ concentrations above 10,000 ppm cause the browning of apples and result in economic loss for farmers. The purpose of this study is to evaluate CO₂ concentrations and their distribution in a controlled atmosphere (CA) storage and provide better structural designs to improve the CO₂ environment using computational fluid dynamics (CFD) simulations. The CFD model was developed for a real CA storage for apples and applied to investigate the effect of changing the inlet and outlet locations and the aspect ratio of the floor of the CA storage on the spatial distributions of CO₂ concentration and the browning of the apples. The lowest CO₂ concentrations in existing CA storage with a high aspect ratio of the floor were achieved from the combination of the inlet located at the top of the right side and the outlet located at the bottom of the left side. In modified CA storage with a low aspect ratio, the combination of the inlet and outlet located at top and bottom of left side respectively achieved the lowest CO₂ concentrations. The proposed case enhanced the storage performance by reducing total browned apples by 3.6% in storage duration of 210 days. This study is expected to reduce the browning damages of apples in CA storage, and thus greatly prevent economic losses.