This paper presents a three-dimensional finite element analysis that couples the high temperature proton exchange membrane fuel cell (HT-PEMFC) and thermoelectric generator into a single model. The proposed model is aimed to accurately simulate this hybrid system by implementing the laminar one-phase flow, concentrated species, ideal gas law physics, electrochemical dynamics of the HT-PEMFC, and the thermoelectric effect of the thermoelectric generator. Furthermore, the thermoelectric generator size, characterized by the number of thermocouple legs, has also been varied to additionally analyze how this parameter will influence the thermoelectric generator and HT-PEMFC’s performances under an identical 353.15 K temperature boundary condition that is representative of domestic hot water. Results show that, for a 7.5 cm by 3 cm fuel cell, increasing the thermoelectric generator size would also increase the current density, heat generated and the output power of the fuel cell. However, higher cathode water and hydrogen concentrations by around 25% and 7% respectively were also found from using a larger thermoelectric generator, which is not favorable from the lifetime perspective. Moreover, adopting a smaller thermoelectric generator size such as the one with 2 pairs of thermocouples increased the thermoelectric generator’s output efficiency to around 1.2%.