To harvest waste heat from flue gas in the industry, this study develops an advanced simulation technology by integrating computational fluid dynamics (CFD) and a thermoelectric module (TEM) where the TEM is modeled as a heat sink to absorb waste heat from flue gases. The influences of Reynolds number, convection heat transfer coefficient at the cold surface, flue gas inlet temperature, dual TEM, and channel geometry on the performance of the TEM system are evaluated. The results clearly provide a measure in increasing the performance of TEM with rising the Reynolds number, flue gas inlet temperature, and convection heat transfer coefficient at the cold surface. In the dual TEM system, the performance of the leading TEM is very close to that of the single TEM, and the dual TEM can produce an additional 43% power when compared with the single TEM. However, this also implies that the output power of the trailing TEM drops 57% when compared to the leading one, stemming for its impact upon the downstream TEM. When the channel geometry is modified to raise the flue gas velocity at Re = 1,000, the output power and efficiency increase by 53.5% and 25.2%, respectively.