This paper considers a microelectromechanical system (MEMS)-based surface-micromachined poly-silicon germanium (poly-SiGe) thermopile, and examines the effects of the geometry of an air tunnel beneath the thermocouple on the effectiveness of its efficiency in energy harvesting. Intended to increase voltage output by enhancing thermal isolation between the two ends of a thermocouple, the air tunnel consists of the upper and lower parts. The upper tunnel results from the elevation of the semiconductor leg and the lower tunnel results from etching the silicon substrate. In our finite element analysis, we parametrized the depth and width of the lower tunnel and the elevation of the upper tunnel to examine the resulting voltage output. We found that, contrary to the intended benefits of thermal isolation effects, the voltage output decreased as the size of the lower tunnel increased. In contrast, voltage output increased as the size of the upper tunnel increased. Based on the above results, we propose that the lower tunnel should be omitted, and the elevation of the upper tunnel should be maximized for higher voltage output.