Thermal management is critically important to maintain the performance of lithium ion battery stacks. In this study, a numerical model and an analytical model for the thermal management of lithium ion battery stacks are developed to investigate the thermal behaviors of flat-plate and cylindrical stacks during discharging processes. It is found that for the same volume ratio of cooling channel and battery of flat-plate design, changing the channel size and the number of channels results in similar average battery temperatures, however, increasing the channel size improves the cooling energy efficiency but leads to more unevenly distributed temperature, and vice versa. The volume ratio of cooling channel to battery needs to be higher than 0.014 for flat-plate design when the Reynolds number of cooling air is around 2000 or higher with a high discharging rate of 2 C. The cylindrical battery stacks considered in this study are generally less compact and more energy-efficient in cooling than the flat-plate battery stacks, and the general thermal behaviors are similar between these two designs. A counter-flow arrangement of the cooling channels or changing the flow direction of the co-flow arrangement periodically may also help the thermal management.