Bamboo-like WO3 nanorods were anchored on three-dimensional nitrogen-doped graphene frameworks (r-WO3/3DNGF) by a facile one-step hydrothermal synthesis plus heating processes. There is a strong dependence of the obtained r-WO3/3DNGF nanostructures on the content of 3DNGF. The composite with 20 wt% 3DNGF content shows the most favorable structure where bamboo-like WO3 nanorods lie flat on the surface of fungus-like 3DNGF, and exhibits a high discharge capacity of 828 mAh g−1 over 100 cycles at 80 mA g−1 with the largest capacity retention of 73.9% for WO3 and excellent rate capacities of 719, 665, 573, 453 and 313 mAh g−1 at 80, 160, 400, 800 and 1600 mA g−1, respectively. The electrochemical performance is better than most of reported WO3-based carbonaceous composites, which can be attributed to the synergistic effects of the following actions: i) WO3 nanorods effectively shorten the diffusion path of Li+; ii) mechanically strong 3DNGF alleviates the huge volume change of WO3 upon Li+ intercalation/extraction; and iii) nitrogen-doping in 3D graphene frameworks improves electronic conductivity and provides large numbers of lithium ion diffusion channels.