Thermal behavior of a Lithium-ion (Li-ion) battery module under a user-defined cycle corresponding to hybrid electrical vehicle (HEV) applications is analyzed. The module is stacked with 12 high-power 8Ah pouch Li-ion battery cells connected in series electrically. The cells are cooled indirectly with air through aluminum cooling plate sandwiched between each pair of cells. The cooling plate has extended cooling surfaces exposed in the cooling air flow channel. Thermal behavior of the battery system under a user specified electrical-load cycle for the target hybrid vehicle is characterized with the equivalent continuous load profile using a 3D finite element analysis (FEA) model for battery cooling. Analysis results are compared with measurements. Good agreement is observed between the simulated and measured cell temperatures. Improvement of the cooling system design is also studied with assistance of the battery cooling analyses. The results of this study demonstrate that the 3D FEA battery cooling model developed in this study can reasonably characterize thermal behavior of the Li-ion battery systems under the dynamic discharge-charge cycle. The correlated FEA model can be used to evaluate and/or optimize the cooling system designs for the battery systems with indirect air cooling.