Raman microscopy was used to investigate microstructural properties of amorphous MoO3 thin films that had been subjected to a photochromic (PC) or electrochromic (EC) process. The Raman spectra changed reversibly when the films went through PC or EC coloration and decoloration cycles. Different molybdenum bronzes were produced with PC and EC treatments, as indicated by the shifts in the Raman bands. The same observation was made in the surface photovoltage spectral experiments. Hence, it was concluded that the microstructure of molybdenum bronze was affected by the coloration means (PC or EC process); the injected cations in an EC process were bonded to the triply coordinated O atoms, whereas the injected H+ ions in a PC process were bonded to both the triply coordinated and doubly coordinated O atoms. The size of the injected cations via EC processes had little effect on the microstructure of the colored films.