The electrochromic properties of WO3 optical windows were improved with a hierarchical structure of amorphous-crystalline WO3 nanowires. The hydrothermal method and sputtering deposition were used for the preparations of crystalline (c-WO3) and amorphous WO3 (a-WO3), respectively. The c-WO3 achieved a high contrast ratio of 55.9% at wavelength 700 nm and had a reversibility of up to 97.5%. The relationship between intercalated/extracted charges and scan time was discussed and formulated. The ion flow variation during charging and discharging was also investigated. The anodic and cathodic current densities of a-WO3/c-WO3 were higher than those of c-WO3 by 7.9% and 30.4%, respectively. The coloration efficiencies were 32.56 cm2-C−1 (improved by 67.2%) at a wavelength of 650 nm, 40.90 cm2-C−1 (improved by 56.1%) at 700 nm, and 58.44 cm2-C−1 (improved by 40.7%) at 800 nm. Rapid redox reaction with short coloring (11.0 s) and bleaching time (6.5 s) was achieved.