Effect of annealing treatment on the refractive index change is observed in fluorinated rigid and semi-flexible chain polyimide film waveguide. The experimental results show that before the completion of thermal imidization, the refractive index change increases rapidly with the annealing temperature and displays a large positive average thermo-optic coefficient. However, after the thermal imidization is completed fully, the refractive index change is slightly submitted to the influence of the annealing temperature and mainly controlled by fluorine content, and there is a negative thermo-optic coefficient in high fluorinated polyimide film with rigidity and in low fluorinated polyimide film with semi-flexibility. In addition, the shortening of the annealing time can lead to enhance the completing thermal imidization temperature. Optical propagation experiment shows the improvement of the light scattering is observed in fluorinated polyimide film waveguide with the completion of thermal imidization.