Using phase change materials (PCMs) is an efficient technique to thermal management of a thermoelectric generator (TEG) system. In this paper a TEG, integrated with PCMs, is investigated and optimized to achieve maximum thermal to electrical conversion efficiency by the TEG. Finite element simulation of the system performance is implemented in Multiphysics simulation environment. The electrical output of the system is compared with the results of experimental procedure, while the experimental and numerical results are in a good agreement. For the optimization process, Taguchi method is used to investigate five critical parameters effective on the system performance to achieve the maximum efficiency. The results show, length to height ratio of the thermoelectric legs has the greatest effect, and length to width ratio of the PCM box has the least effect on the conversion efficiency of the system. While 540 kJ thermal energy is applies to the system during 1800 s, an average conversion efficiency of 4.28% is obtained during 6000 s of the heating and cooling stages.