Abstract The thermal and electrochemical performance is seldom discussed for a battery module using heat pipe cooling. A three dimensional battery module model, including conjugated heat transfer sub-model, multi-cell sub-models and heat pipe sub-model for a serially connected battery module using heat pipe cooling, is developed and experimentally validated. The electrochemical-thermal characteristic is correspondingly considered for each cell. The dynamics of temperature, local current density, Li+ concentration and voltage are studied in cooling process with different coolant temperatures. With coolant temperature reducing, the temperature difference of the module increases although the maximum temperature decreases. The cell near to the inlet has larger local temperature difference. Under different coolant temperatures, both the local current density and Li+ concentration initially show little variation. Subsequently, those under lower coolant temperatures changes more violently, forming a larger spatial gradient within a cell. Compared with that in anode, the gradient of solid phase Li+ concentration in cathode is more sensitive to the coolant temperature and dominates the loss of available capacity when reducing coolant temperature. The voltage of the battery module decreases and the available capacity decreases by about 0.88%–1.17% with reducing coolant temperature by 10 °C at 5C discharge.