WOx electrochromic (EC) films deposited by DC magnetron sputtering technique were investigated by XRD and STM measurements. The reversible microstructure changes of the WOx film between the bleached and colored EC states were revealed. The study indicates that the amorphous as-deposited WOx film (a-WOx) is of amorphous microstructure both in bleached and colored states; however, the crystalline WOx (c-WOx) is stoichiometric triclinic lattice WO3 in bleached state (the lattice parameters: a=7.2944 Å, b=7.4855 Å, c=3.7958 Å, α=89.38°, β=90.42°, γ=90.80°), and changes into nonstoichiometric tetragonal lattice WO2.9 in colored state (a=b=5.336 Å, c=3.788 Å, α=β=γ=90°). The surface morphologies of the colored WOx films are very different from those of the bleached WOx films.