The effective utilization of renewable energy has become critical to technological advancement for the energetic transition from fossil fuels to clean and sustainable sources. Ocean Thermal Energy Conversion (OTEC) technology, which generates electricity by leveraging the temperature differential between surface and deep ocean waters, enables stable power generation around the clock. In this domain, the combination of thermoelectric generators (TEGs) and heat exchangers has exhibited immense potential for ameliorating the deficiencies of conventional OTEC. This study uses finite element numerical simulation of the COMSOL5.5 software to investigate the fluid dynamics characteristics of heat exchangers with flat fins and different types of longitudinal vortex generators (LVGs) under the same number of fins. This research encompasses heat exchangers with rectangular, triangular, and trapezoidal LVGs. Concurrently, the analysis examines how the vortices generated by the LVGs influence the thermoelectric performance of the TEGs. The results demonstrate that heat exchangers integrating flat fins and LVGs can enhance the power generation efficiency of TEGs. However, the pumping power required by the LVGs constrains the thermoelectric conversion efficiency. Compared to rectangular and triangular LVGs, trapezoidal LVGs achieve a superior balance between output and pumping power. Heat exchangers utilizing trapezoidal LVGs can attain the highest TEG thermoelectric conversion efficiency with a specific seawater flow velocity. Overall, these findings provide valuable reference information for applying TEGs and heat exchangers in OTEC design.