This paper presents a numerical model of an exhaust heat recovery system for a high temperature polymer electrolyte membrane fuel cell (HTPEMFC) stack. The system is designed as thermoelectric generators (TEGs) sandwiched in the walls of a compact plate-fin heat exchanger. Its model is based on a finite-element approach. On each discretized segment, fluid properties, heat transfer process and TEG performance are locally calculated for higher model precision. To benefit both the system design and fabrication, the way to model TEG modules is herein reconsidered; a database of commercialized compact plate-fin heat exchangers is adopted. Then the model is validated against experimental data and the main variables are identified by means of a sensitivity analysis. Finally, the system configuration is optimized for recovering heat from the exhaust gas. The results exhibit the crucial importance of the model accuracy and the optimization on system configuration. Future studies will concentrate on heat exchanger structures.