In this study, WO3 crystal structure films were deposited on conductive glass (FTO) by seed layer assisted hydrothermal reaction method. Through controlling the concentration of hydrochloric acid, oxalic acid, the hydrothermal postprocessing temperature, the Micro-peony, Micro-Urchin like, and porous petal like WO3 crystal structures were obtained respectively. Scanning electron microscopy (SEM), X-ray diffraction (XRD), transmission electron microscopy (TEM) and electrochemical characterization were used to study the formation mechanism of different structures and their effects on the electrochromic properties of WO3 films. Cl- in HCl has a strong promoting role towards the c axis in WO3 crystal growth and oxalic acid has promoting effect towards an axis. In terms of color efficiency, the CE value of micro-urchin is 42.37 cm2 C-1, far greater than that of two other WO3 structures, 15.21 cm2 C-1 and 12.71 cm2 C-1. Due to the cold-water quenching treatment, the CE value of WO3 micro-peony with porous surface structure was 56.95 cm2 C-1, 4 times of the smooth surface structure in CE, slightly better than the micro-urchin structure.