Three-dimensional (3D) hierarchical heterostructures have been widely studied for energy storage because of their amazing synergistic effect. However, a detailed characterization how the branched structure affects the backbone structure during electrochemical cycling, and the specific relationship between the backbone and the branched heterogeneous structure (namely synergistic effect) have been rarely revealed. In addition, the controllable synthesis of this system still remains a great challenge. Herein, we developed a one-step gradient hydrothermal method to obtain a series of 3D hierarchical heterogeneous nanostructures, including V2O5/NaV6O15, V2O5/ZnV2O6 and V2O5/CoV2O6, through controlling the sequence of nucleation and growth processes of different structural units in the same precursor. On the basis of time-resolved in situ X-ray diffraction (XRD) characterizations, we clearly elucidated the synergistic effect between the branched and backbone structure. During the synergistic effect, the branched NaV6O15 helps to reduce the potential barrier during lithium-ion insertion/extraction, buffers the impact of crystal-system transformations during the charge/discharge process; the backbone V2O5 is beneficial to increase the charge/discharge capacity, inhibits the self-aggregation of branched NaV6O15 and maintains the stability of 3D structure. Consequently, 3D V2O5/NaV6O15 hierarchical heterogeneous microspheres exhibit the best electrochemical performance than pure V2O5 and V2O5/NaV6O15 physical mixture in lithium-ion batteries (LIBs). When tested at a high rate of 5Ag−1, 92% of the initial capacity can be maintained after 1000 cycles. We believe this method will be in favor of the construction of 3D hierarchical heterostructures and this specific synergistic effect investigated by in situ XRD will be significant for the design of better electrodes.