The most important premise of thermoelectric generator (TEG) system is a large enough temperature difference. The effects of cooling method on the temperature difference at the two end of TEG were thus studied through building an energy recovery simulation system for engine cooling system based on the thermoelectric generation technology. The results show that the temperatures of hot and cold end are the same and increase before and after starting the full circulation. There is a temperature difference between the coolant and hot end due to the thermal resistance of heat collector, but the difference is very small due to the conduction of TEG. It also shows that the forced air cooling method can increase the TEG temperature difference. Compared with the side cooling, the front cooling is more beneficial, but it can only cool one single surface. The method of connecting the cold end and radiator with heat pipe is applied so that the temperature at the cold end further decreases and then the temperature difference becomes large. It is concluded that the cooling method has great influence on the temperature difference of energy recovery system.