As environmental regulations on exhaust gas are being enforced around the world, and marine transportation is gradually being strengthened. It is believed that various methods will be attempted to the emission regulations. The thermoelectric power generation system can convert thermal energy into electrical energy. It can be applied without limiting the functions of the equipment and parts in the existing ship and has the advantage of not incurring large maintenance costs, which have spread to ship applications. In order to optimize the design of the thermoelectric power generation system, the heat transfer phenomenon due to the internal position was analyzed through CFD, and cross-validation was carried out through comparison with actual experimental values. Before conducting CFD of the thermoelectric power generation system, By setting the porous domain for the fin was applied to TEM to derive accurate results while reducing the calculation load. Comparing the fin that was applied to TEM and porous domain CFD results confirmed that the fin and porous domain CFD results have a great agreement with a maximum error of less than 0.5%. After that, performed a CFD of the entire thermoelectric power generation system, analyzed the heat transfer phenomena in a thermoelectric generator, and based on the results, conducted a comparison verification with the experimental results. The result of the comparison indicates the maximum error in the cooling jacket and power generation. This is analyzed in the experimental and CFD adiabatic efficiency difference, the heat loss difference at different locations in the actual experiment. In this study establishes an analysis methodology through comparative verification of experiments and CFD, It is expected that can optimize the design of thermoelectric power generation systems through the established methodology.