The automotive exhaust-based thermoelectric generator integrated with a three-way catalytic converter (TWC) can convert the thermal energy of exhaust gas into an electric energy, and solve the compatibility issues with an exhaust system. More power can be generated when the temperature of heat exchanger is higher. However, the performances of TWC are also affected by the temperature of the heat exchanger. To get more power generation and reduce the impact on the TWC, three heat exchangers with different section shapes were simulated and corresponding surface temperature and back-pressure were compared. Then three kinds of fins were employed in heat exchangers to figure out the effects. Finally, the results showed that the section shape had no obvious effect on the distribution of temperature and pressure in heat exchangers, but the arrangement of the fins inside the heat exchanger had a heavy impact on the performance of the heat exchanger. According to the simulation results, the heat exchanger in which the direction of fins was skewed to the streamwise could get higher temperature and output power at 192.96 W.