The maximum generated power of automobile exhaust thermoelectric generator (AETEG) can be enhanced by applying inserted fins to its heat exchanger, for the temperature difference of thermoelectric modules (TEMs) is increased. However, the heat exchanger will result in undesired backpressure, which may deteriorate the performance of the internal combustion engine (ICE). To evaluate the backpressure on the performance of both the ICE and the AETEG, the model of ICE integrated with AETEG was established with the GT-power software and validated with the AETEG test bench. The heat exchangers with chaos shape and fishbone shape were proposed, their pressure drop with different engine speeds was studied, and their effects on the performance of both the AETEG and the ICE were analyzed. The results showed that compared with the fishbone-shaped structure, the pressure drop of chaos-shaped heat exchanger is larger at the same engine speed, which contributes to the increased maximum power and hot side temperature of the AETEG. Moreover, compared with the ICE without heat exchanger, the brake torque, brake power, volumetric efficiency and pumping mean effective pressure of the ICE assembled with chaos-shape and fishbone-shape heat exchanger reduce, and the corresponding brake specific fuel consumption, CO emission and CO2 emission increase because of the raised backpressure caused by the heat exchanger.