The 3D Thermal modeling utilizes a Finite Differencing heat alteration method augmented with empirical boundary conditions is employed to develop 3D thermal model for the integration of thermoelectric modules with proton exchange membrane fuel cell stack. Hardware-in-Loop was designed under pre-defined drive cycle to obtain fuel cell performance parameters along with anode and cathode gas flow-rates and surface temperatures. The fuel cell model is used to conjugate the experimental boundary conditions with the Finite Differencing code, which implemented heat generation across the stack to depict the chemical composition process. The structural and temporal temperature contours obtained from this model are in compliance with the actual recordings obtained from the infrared detector and thermocouples. The model is harmonized with thermo-electric modules with a modeling strategy, which enables optimize better temporal profile across the stack. This study presents the improvement of a 3D thermal model for proton exchange membrane fuel cell stack along with the interfaced thermo-electric module. The model provided a virtual environment using a model-based design approach to assist the design engineers to manipulate the design correction earlier in the process and eliminate the need for costly and time consuming prototypes. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.