The current air-cooled battery energy storage system has low cooling efficiency, large temperature difference between batteries, and much heat accumulation, which affects the safe operation of battery energy storage system. In order to improve the cooling efficiency of the battery energy storage system, this study focuses on the influence of the cold aisle structure on the air-cooled cooling efficiency of a containerized energy storage system. By building a three-dimensional CFD model, the study focuses on the influence of the cold aisle structure (open/closed), the air supply mode (underfloor air supply/inter-column air conditioning air supply), and the layout of the air outlets (back/side) on the temperature field of the battery energy storage system. The results show as follows: the closed cold aisle structure can significantly improve the airflow organization uniformity and reduce the maximum temperature difference on the surface of a single cell to 5.1 ℃, which is 15% (0.9 ℃) lower than that of the open structure; the under-floor air supply controls the temperature difference of the cell to 5.1 ℃, which is 8.9% less than that of the horizontal air supply mode of the column air conditioner; the maximum temperature difference of the system can be reduced to 4.9 ℃when the air outlet adopts the back exhaust design, which improves the cooling efficiency by 4.1% and 3.2% compared with the left and right side air outlet schemes, respectively. This study provides valuable guidance for the thermal management design of battery energy storage systems, especially in improving system safety and performance.