High transmittance and low birefringence are desirable optical properties in polyimide films which are promising flexible substrates in next generation display devices. However, thermal processes for the fabrication of polyimide films can cause anisotropic changes in the optical properties due to its rod-like molecular structure. Here we report the changes in optical retardation in transparent fluorinated polyimide films with sub-nanometer resolution and dimensional stability induced by deformation at high temperatures. As deformation is increased, the optical retardation is changed much prominently with enhancing thermo-dimensional stability. During thermal strain, in-plane molecular orientation is preferentially improved and stress-optical coefficient that quantifies the change in out of plane optical retardation is derived to be around 6×10?6 m2/N, which is higher compared to conventional plastic optical films. The experimental findings suggest that optimized process conditions for display substrates should be determined to address both changes in the optical and thermal stabilities. We suggest that this study can be useful information for large-scale film process to be further utilized in fabrication of the transparent polyimide films.