In situ study of the annealing effects, up to 600 °C, upon the optical performance of SnO2:F films have been successfully conducted with spectroscopic ellipsometry. The thickness and optical parameters were obtained by the regression of the measured ellipsometry parameters using a five-layer model. The results show that the re-densification of the SnO2:F layers occurs at above 200 °C, resulting in an irreversible thickness reducing from about 326 nm to about 321 nm. The refractive index of the SnO2:F layer increases with temperature and decreases in the cooling period. The in situ temperature dependence of the average refractive index has a good agreement with the sheet resistance measurement results, not only verifying the annealing process deteriorates the low-emissivity performance, but also demonstrates that spectroscopic ellipsometry method is a suitable optical characterization technique to adjust the on-line coating process of float glass.