Suitable host structure for lithium insertion and extraction is crucial for lithium-ion batteries. Tungsten trioxides (WO3) are particularly interesting materials for this purpose. In this work, the influences of structure and composition of WO3 on the charge/discharge performances of Li-ion batteries are systematically investigated. Firstly, lithiated tungsten trioxides (Li-WO3) are successfully synthesized by a hydrothermal method followed by annealing at different temperatures (200–600°C). It is found that the hexagonal framework collapses and gradually transforms to the monoclinic phase due to the release of NH4 + and NH3 molecules. Unexpectedly, monoclinic WO3 reveals better performances than that of hexagonal WO3. Among all the investigated samples, the lithiated WO3 annealed at 500°C exhibits the highest discharge capacity and cycle performance (703mAhg−1 after 10 cycles). We believe that the Li+ remained in the solid structure of WO3 can lead to a more stable structure. In addition, Li+ could inhibit the oxidation of W5+ during the heat treatment process, which increases the electron conductivity of WO3. Our results indicate that the electrochemical properties of WO3 are strongly related to the residual precursor and crystal structure.