A hybrid power composed of fuel cell and batteries has become the good strategy for HEV. On the contrary, the produced heat of batteries can affect to the total performance of HEV significantly. In this study, simulation methods with optimization were developed for obtaining the high performance cooling system of batteries. At first, a numerical method for obtaining the temperature distribution of batteries was developed by using CFD. In the following step, several parameters were investigated for selecting design variables with the important effect on the performance of the cooling system of batteries. Finally, an optimization method based on DOE and RSM was obtained through a real optimal design. There was 21.1% reduction on the view of the root mean square temperature between batteries as shown in the optimization result. The developed analysis with optimization can be used to improve the performance of the cooling system of batteries, and these works have made the theoretical basis for simulation and optimization of the cooling system of batteries.