Recently, cylindrical lithium-ion battery cells have been widely used in electric vehicles due to efficient automated production and cheap kilowatt-hour capacity. For optimal operation of a cell, the internal temperature of the cell should be maintained within the range of 15–35 °C by employing suitable cooling mechanism. This study comprehensively compares multiple air-cooling configurations specifically designed for lithium-ion battery three-series and three-parallel (3S3P) modules using. The methodology involves an experimental phase to measure the parameters of Bernardi's equation, essential for calculating heat generation with consideration of both Joule's heat and entropic heat. Subsequently, a numerical simulation using Ansys Fluent examines battery heat generation within the 3S3P modules, employing diverse air-cooling configurations. Each configuration undergoes simulation with the aid of design of experiments and parametric analysis, allowing the observation of cooling behavior across various input parameters. To ensure reliability of simulation, the cooling of the unit cell module is simulated under similar conditions. The comparison between these simulated results and experimental values is conducted to validate the accuracy of the overall analysis methodology. The heat measurements indicated a unit cell heat output of 0.9028 W at an average rate of 0.85C. Among the investigated air-cooling configurations, the SIDO (Single Input Double Output) arrangement stood out as the most effective in maintaining a consistently lower average cell temperature, as determined through the application of the response curve method. This study emphasizes the importance of air-cooling design for improving the performance and safety of lithium-ion battery modules used in electric vehicles.