An astigmatic optical profilometer is a precision instrument with advantages such as high resolution, high bandwidth, a compact size, and low cost. However, current astigmatic optical profilometers measure only surface morphology, and their potential for capturing subsurface information remains underutilized. In this study, we developed a method for measuring the thickness of transparent thin films with an astigmatic optical profilometer. Experimental results demonstrate that the thickness of transparent films tens of micrometers thick can be accurately measured. The maximum thickness measurable through our system is approximately 100 μm, which may be increased to 1.2 mm through the use of a scanner with a greater travel range. A coupling problem occurs for films <25 μm in thickness. However, to solve this problem, we devised a decoupling method, which was experimentally implemented to successfully measure a 18-μm-thick film. Moreover, the ability to obtain 3D images, including of both the upper and lower surfaces, was demonstrated.