Thermal lens microscope (TLM) is a sensitive detection method for nonfluorescent molecules and widely applied to detection in a capillary or on a microchip. In this paper, we developed a flexible design tool for TLM systems to meet various applications utilizing a microspace. The TL effect was modeled, including signal processing, and calculated by combining fluidic dynamics and wave optics software. The coincidence of the calculations and experiments was investigated by measuring the effects of optical path length or focus positions of the excitation beams on TL signals which are quite difficult to calculate by a conventional method. Good agreement was shown and the applicability of the TLM design tool was verified.