To understand the thermal effect of polymer Li-ion cells during the discharge process, an electrochemical thermal coupling model was established to investigate the thermal behavior of the cell. The average deviation and variance between the modeling results and the experimental data at 3C discharge rate were 0.57 K and 0.15, thus it was concluded that the modeling results agreed well with the experimental data. Also, the model is used to analyze the temperature distribution affected by discharge rate and cooling condition. The average heat production rate of the cells shows an increasing trend throughout the discharge process; it is increased significantly at both the beginning and the end of discharge. At a high discharge current, the irreversible heating which is proportional to the square of the current density, is the major heat generation source inside the battery. At a low discharge current, the heat production rate is dominated by reversible entropic heat. Improving cooling temperature could lower the average temperature during the discharge process. When the heat coefficient is 5 W/(m2·K), the average temperature rises of the battery cells are 6.46 K, 17.67 K, 27.53 K for 1C, 3C, 5C discharge rates respectively. If the heat coefficient increases to 25 W/(m2·K), the average temperatures of the battery cells are reduced by 2.91 K, 4.68 K, 5.62 K for 1C, 3C, 5C discharge rates, respectively, but the inner temperature difference would be increased.