In the present study, the thermal and electrical performances of automotive waste heat recovery thermoelectric generator system are investigated for different internal fin structures in hot heat exchanger. A coupled numerical model integrated with heat transfer and thermoelectric effects is developed to simulate the Multiphysics behavior of thermoelectric generator system. The coupled numerical model is validated with experimental results for both thermal and electrical performances within maximum error of ± 8%. The temperature difference, pressure drop, power, conversion efficiency, exergy efficiency, and net efficiency of thermoelectric generator system are compared for hot heat exchanger without internal fin structure and that with 12 different internal fin structures. The 12 different internal fin structures comprise of straight fins, perpendicular fins, fishbone fins, triangular guide fins, and combination of fins. The results reveal that, an Internal structure11 depicts superior thermal and electrical performances of thermoelectric generator system among all internal fin structures. Despite of higher pressure drop of 0.04571 bar, the Internal structure11 shows superior power, conversion efficiency, exergy efficiency, and net efficiency of 70.79 W, 7.76%, 14.10%, and 0.996%, respectively. The hot heat exchanger with Internal structure11 is proposed as the best configuration for the optimum performance of thermoelectric generator system.