Cooling of the Li-ion battery module is a critical issue for electric vehicles in regard with the battery performance and lifetime, particularly at abused operating conditions. A water cooling system consisting of two novel cover plates with T-shape bifurcation structures and eight traditional cold plates was proposed and investigated for cooling of prismatic LiFePO4 battery modules. A computational fluid dynamics simulation model of the cooling system was established and validated by experimental data. The results show that a cold plate with four circular mini-channels flowing water can keep the maximum temperature of a single battery around 35 °C at 1 °C discharging rate and ambient temperature of 40 °C. Effect of the coolant flow rate is much less significant than the inlet coolant temperature on the cooling performance. Two sets of the proposed water cooling systems can significantly reduce the maximum temperature of a battery module consisting of 15 batteries. Moreover, great temperature distribution uniformity between different batteries can be achieved because the novel cover plate is able to distribute water evenly into each mini-channel of the cold plates. The cooling system can keep the maximum temperature of the module below 32.5 °C and the difference between the highest and lowest temperatures around 1.5 °C at abused operating conditions.