To better manage the magnitude and the direction of the heat flux in an exchanger-based methanol evaporator of a fuel cell system, thermoelectric (TE) modules can be deployed as TE heat flux regulators (TERs). The performance of the TE-integrated evaporator is strongly influenced by its heat exchange structure. The structure transfers the fuel cell exhaust heat to the evaporation chamber to evaporate the methanol, where TE modules are installed in between to facilitate the heat regulation. In this work, firstly, a numerical study is conducted to determine the working currents and working modes of the TERs under the system working condition fluctuations and during the system cold start. A 3-dimensional evaporator model is generated in ANSYS FLUENT® by combining a compact TE model with various heat exchange structure geometries. The compact TE model can dramatically improve the computation efficiency, and uses a different material property acquisition method based on module manufacturers’ datasheets. Secondly, a simulation study is carried out on the novel evaporator to minimize its thermal resistance and to assess the evaporator pressure drop. The factors studied include: type of the fins of the heat exchange structure, thickness of the fins, axial conduction penalty, etc. Results show that the TE-integrated evaporator can work more efficiently and smoothly during both load fluctuations and system cold start, it is of superior performance.