In this work, WO₃ crystal structure films are deposited on conductive glass substrates by seed layer assisted hydrothermal reaction method. Through controlling the concentration of hydrochloric acid, oxalic acid, and the hydrothermal postprocessing temperature, the micro-peony, micro urchin-like, and porous petal-like WO₃ crystal structures are obtained respectively. Scanning electron microscopy (SEM), X-ray diffraction (XRD), transmission electron microscopy (TEM) and electrochemical characterization are used to study the formation mechanism of different structures and their effects on the electrochromic properties of WO₃ films. The Cl^– in HCl has a strong promoting role towards the c axis in WO₃ crystal growth and oxalic acid has a promoting effect towards an a axis. In terms of color efficiency, the CE value of micro-urchin is 42.37 cm²/C, far greater than those of two other WO₃ structures, 15.21 cm²/C and 12.71 cm²/C. Owing to the cold-water quenching treatment, the CE value of WO₃ micro-peony with porous surface structure is 56.95 cm²/C, quadruple CE value of the smooth surface structure, slightly better than that of the micro-urchin structure.