Abstract The temperature gradient due to the battery cooling thermally drives the unbalanced discharging of a battery module, which is seldom discussed. The shortcoming of the previous modeling methodology of modules also limits the discussion. A multilayer electrochemical-thermal model considering parallel connected cells inside each battery is developed for a serially connected module to investigate the unbalanced discharging with the cooling incorporated. The unbalanced discharging intensifies significantly after the depth of discharge exceeds about 0.8. The unbalanced discharging is the most susceptible to the non-uniform cooling when the cooling performance exactly reaches to the stage of slight improvement. The discharging rate slightly aggravates the unbalanced discharging after 4 C. Reducing the initial temperature of the module exponentially aggravates the unbalanced discharging, which will increase by about 100% when the coolant temperature reduces by 5 °C. The local temperature difference of a battery aggravates the unbalanced discharging, especially when each battery has various local temperature differences. Increasing the cell number will reduce the unbalanced discharging and the reduction will be insignificant when the improvement of cooling performance becomes slight with the convective heat transfer coefficient increasing. The results are helpful to the design of cooling configurations, cooling control strategy and equalization method.