Tungsten trioxide (WO3) is an indirect bandgap semiconductor and has been identified as one of the most promising inorganic working electrode materials for electrochromic, electrocatalytic, photocatalytic and sensing application. In this paper, vertically aligned hierarchical WO3 nano-architectures on transparent conducting fluorine-doped tin oxide (FTO) glass were prepared by a facile template-free crystal-seed-assisted hydrothermal method. The effects of the hydrothermal temperature, reaction time and capping agents on the crystal structure and morphology of the products were investigated by X-ray diffraction (XRD) X-ray photoelectron spectroscopy (XPS) and scanning electron microscope (SEM). The XRD studies showed that the as-prepared thin films obtained below 150℃ were comprised of orthorhombic WO3·H2O and were completely converted to monoclinic WO3 at 180℃. It was also noted that there was a phase transformation from orthorhombic to monoclinic by increasing the reaction time from 1h to 12h. SEM analysis revealed that WO3 thin films composed of rodlike, wedgelike, and platelike nanostructures could be selectively synthesized by adding NaCl, K2SO4, and H2C2O4 as capping agent. It was found that oxalic ion play an important role in the formation of vertically aligned platelike arrays. Due to the vertically aligned structure and the porous space among the nanorods or nanoplates, which make the diffusion of H+ in the arrays easier and provide much more active reaction area, the WO3 nanostructure films exhibits advantageous electrochemical abilities.