A MoO3–MnO2 intergrown nanoparticle composite was synthesized by a one-step hydrothermal method. X-ray diffraction, transmission electron microscopy and X-ray photoelectron spectroscopy analyses show the biphasic intergrown nanocrystalline particles of MoO3 and MnO2 with a narrow size distribution ranging from 6 nm to 8 nm. The main feature of the intergrown structure is the synergistic effect of MoO3 and MnO2 during intergrowth in the hydrothermal process. Mo(6+) is embedded into MnO2 to support its crystal lattice, whereas Mn(4+) is incorporated into the MoO3 lattice to modify its crystal structure. The synergistic intergrowth of the biphases greatly improves the structural stability and its electrical conductivity of the MoO3–MnO2 composite. The composite attains an initial specific capacity of 2034.2 mAh g−1 and stays 1446.5 mAh g−1 after 50 cycles at a rate of 0.5C in the voltage range of 0.01–2.0 V in lithium-ion batteries. Even at a high rate of 1.0C the capacity remains at 624.2 mAh g−1 after 150 cycles. Therefore, the fabricated MoO3–MnO2 intergrown nanoparticle composite is a promising anode material for lithium-ion batteries. The proposed one-step hydrothermal method for the synthesis of biphasic intergrown nano-composite can be used as a general approach to prepare other electrode materials for electrochemical applications.