Tunable polymer microlens has been widely applied in many fields such as imaging, microfluidic sensing and adaptive optics. The physical model for controllable polymer microlens caused by thermal effect is established. Then, the finite element method (FEM) is used to analyze the spatial distribution of the microlens temperature, thermal deformation and focal length variation. The simulation results show that the thermo-optic effect has a strong influence on the optical performance of polymer microlens with large thermo-optic coefficient when the variation scope of temperature is relatively large. As a result, both thermal expansion effect and thermo-optic effect should be taken into account for the design and fabrication of such devices.