To improve the accuracy of heat exchanger computational fluid dynamics (CFD) simulations, the transverse resistance coefficient of the cold side and the hot side of the water-cooled charge air cooler (WCCAC) is calculated using the fin element method, and the influence of several common factors on the resistance coefficient of the fin element is analyzed. The transverse resistance coefficient obtained from the simulation of the fin element is substituted into the WCCAC model and compared with experimental data. It was found that the fin element method can simulate the flow field of the WCCAC accurately, and the simulation results were closer to the experimental curve compared with the empirical method. This study provides guidance for the optimal design of the heat exchanger and is helpful to shorten the development time and to save costs.