The adoption of fully electric ships represents a significant step forward in addressing the environmental challenges of climate change and pollution in the shipping industry. This research details the optimized design of a battery energy storage system (BESS) and its air-cooling thermal management system for a 2000-ton bulk cargo ship. In comparison to the conventional flow splitter (FS-I), which divides airflow into 8 transverse branches, two novel designs—FS-II (dividing airflow into 2, 4, and 8 branches) and FS-III (dividing into 2, 4, 8, and 16 longitudinal and transverse branches)—were introduced. FS-II improves flow uniformity from 0.42 (FS-I) to 0.86 but results in an increased pressure drop up to 881.47 Pa. FS-III further enhances flow uniformity to 0.97 while reducing pressure drop to 191.99 Pa. The thermal performance of battery boxes with FS-I, FS-II, and FS-III was evaluated under extreme conditions and a complete voyage cycle. FS-III exhibited superior thermal regulation, maintaining Tmax consistently below 33.9°C during the entire voyage. These findings provide valuable insights for designing thermal management systems in electric ships.