In this paper, we present modeling and simulation of microlens formation by means of a deep X-ray lithography followed by a thermal treatment of a PMMA (Polymethylmethacrylate) sheet. According to this modeling, X-ray irradiation causes the decrease of molecular weight of PMMA, which in turn decreases the glass transition temperature and consequently causes a net volume increase during the thermal cycle resulting in a swollen microlens. In this modeling, the free volume theory including the relaxation process during the cooling process was considered. The simulation results indicate that the modeling in this study is able to predict the fabricated microlens shapes and the variation pattern of the maximum heights of microlens which depends on the conditions of the thermal treatment. The prediction model could be applied to optimization of microlens fabrication process and to designing a micro mold insert for micromolding processes.