To enhance the performance of the automobile thermoelectric generator (ATEG), this study proposes a heat exchanger with dimple fins, where the number of dimples systematically increases along the direction of exhaust flow. The innovative combination of dimples with fins effectively addresses the impact of temperature reduction in the exhaust. The distribution of dimples on the fins is optimized based on a fluid-thermal-electric multiphysics model and a net power model. According to simulation results, it can be found that as the number of columns and radius of the dimples increase, the ability of the heat exchanger to transfer heat is improved while the back pressure loss of the exhaust flow is also increased. Through optimizations, the optimal dimple distribution of n = 8 and r = 1.45 mm is obtained, achieving a maximum net power output of 62.46 W. The performance of the optimized ATEG with dimple fins is greatly improved in comparison with the conventional plate-fin structure, and its conversion efficiency, output power, output voltage, and net power output are increased by 16.07 %, 28.95 %, 13.56 %, and 10.09 %, respectively. The results of this study offer valuable guidance for shaping the heat exchanger’s design.