This paper enhances the thermal uniformity of the thermoelectric generator (TEG) system utilizing diesel engine exhaust gas by optimizing muffler inlet and outlet structures. Two series of computational fluid dynamic simulations at three engine operating modes were conducted to investigate the effects of their diameters and positions on the distribution of the hot-side heat exchanger (HSHE) temperature. The weighted average method was used to select the set of optimal parameters. The results indicate that these structural parameters affect the temperature uniformity on the HSHE base through impact on the exhaust velocity distribution inside the muffler. The optimal model with the inlet diameter of 35mm, outlet diameter of 40mm, and the inlet and outlet positions, respectively, 40mm and 34mm from the muffler centerline, achieves temperature differences across cross-sections of only 1.56K to 2.61K at an engine speed of 1920 rpm and torque of 31Nm. This finding enhanced temperature uniformity by 36.2% compared to the worst model in this study. The optimal muffler inlet and outlet structures obtained in this study offer the foundation to improve the longitudinal temperature uniformity of the TEG system, resulting in strengthening system performance and life span.