Heating and annealing effects on the optical properties of slightly blue substoichiometric molybdenum trioxide thin films are reported partially. During heating and annealing, different levels of coloration seem to be generated by simultaneous reduction and proton injection into thin films, which cause the formation of hydrogen molybdenum bronzes of different concentrations. The optical band gap, Eo, of MoO3 thin film when annealed in between 313 and 473 K is decreased to 2.82 eV, and this reduction in Eo has been explained with a view to phonon and polaron species. Moreover, temperature-dependent change in the optical band gap has also been interpreted in terms of band gap slope, B, and the real part of the refractive index, n. Urbach slope, σ, also goes down to 0.67 eV−1 due to annealing treatment. Using the oscillator model, a phonon energy, hνo, of about 0.08 eV was found for the reported MoO3 thin film which is very close to the characteristic phonon energy of MoO3. Over and above, the intensity for the blue absorption band, over the photon energy range 0.4–3.0 eV, also reaches a maximum as MoO3 thin film is annealed at 473 K for 1 h and then decreases by 32% after annealing at the same temperature for 2 h. This phenomenon is due to polaronic band intensity which rises and falls during annealing. Half-width of the blue band, as found by fitting polaron model, is changed only by 3% on annealing the MoO3 thin film at 473 K as compared to its value at room temperature.