The potential for automotive exhaust-based thermoelectric generator (TEG) has been increasing with continuously advances in thermoelectric technology. In this paper, the thermal deformation of the TEG system is studied on the basis of the surface temperature distribution of the heat exchanger. The simulation result shows that thermoelectric modules (TMs) on different positions have different thermal performance which can significantly influence the power generation efficiency of the system. Meanwhile, in terms of the working performance of TMs, the clamping mechanism is considered to have some effects on both the cold side and the hot side of TEG. Following the simulation, bench tests are carried out to confirm the reasonability of the simulation results. Based on the results of the simulation and the experiment, it can be put forward that the TM will achieve better thermal performance with optimization of the clamping mechanism, which is practically helpful to enhance the working performance of the TEG.