Fluffy ultrathin WO3 nanoneedle clusters are in-situ grown in mesoporous hollow carbon nanospheres (MHCSs) via unique material impregnation and confined molten reaction in MHCS nanoreactors. Through transmission electron microscopy, scanning electron microscopy, X-ray diffraction, Raman spectra and X-ray photoelectron spectroscopy analyses, it can be found that WO3 nanoneedles with 5–10 nm in thickness and ∼140 nm in length are encapsulated within each MHCS with 150–250 nm in diameter and 30–40 nm in shell thick. Thermal gravimetric analysis reveals the WO3 content of 83.5 wt%. Lithium storage performance was evaluated by galvanostatic charge/discharge cycling, cyclic voltammogram and electrochemical impedance spectroscopy. The composite exhibits remarkable rate performance (average discharge capacity of 1352 mAh g−1 at 0.1 A g−1 and 105 mAh g−1 at 10 A g−1) and excellent cycling performance (1094 mAh g−1 at 0.2 A g−1 after 50 cycles, 760 mAh g−1 at 1 A g−1 after 500 cycles, 351 mAh g−1 at 5 A g−1 after 2000 cycles). The composite also presents outstanding kinetics properties, such as high Li+ diffusion coefficient, strong capacitive effect, and low electrochemical impedance. The superior electrochemical performance is attributed to unique “ship-in-a-bottle” structure. MHCSs facilitate electron transfer and ion diffusion, buffer volume change of WO3 and maintain the integrity of WO3. Furthermore, fluffy ultrathin nanoneedle cluster structure endows WO3 with high electrochemical activity.