In this paper, the temperature of coupling system including cylinder, head, inlet/exhaust valve, and the cooling jacket of a 400cc engine is investigated by computational fluid dynamic (CFD) method. Firstly, the total pressure loss of water jacket, radiator, and thermostat is calculated first, and then the mass flow rate inside the cooling system can be determined by fitting the water pump’s performance curve (P-Q curve). The thermal boundary conditions for analysis of conjugate heat transfer of cooling system, such as combusting gas temperature and heat transfer coefficient are utilizing the results of 1-D engine simulation software (Ricardo WAVE). The current approach is that the heat transfer coefficients of valve while opening are calculated by considering the intake and exhaust stroke using FLUENT to overcome the difficulty of these values that are not modeled in such 1-D software. Finally, the finite element method (FEM) is used for the valve stress calculation.The results indicate that the temperature, pressure loss and the flow rate of coolant exhausted from the cooling jacket are concurred with those of experimental results. In addition, the distributions of convective heat transfer coefficients of valves are found to have different behavior for five sections of valve defined in this study. Therefore, this method is expected to predict the transient temperature distribution of valve seats and valves with a high degree of accuracy. The results show that maximum valve stress can be found in the seat face of the intake/exhaust valves because of the thermal gradient.