Germanium based nanomaterials are very promising as the anodes for the lithium ion batteries since their large specific capacity, excellent lithium diffusivity and high conductivity. However, their controllable preparation is still very difficult to achieve. Herein, we facilely prepare a unique carbon coating Ge nanospheres with a cubic hollow structure (Ge@C) via a hydrothermal synthesis and subsequent pyrolysis using low-cost GeO2 as precursors. The hollow Ge@C nanostructure not only provides abundant interior space to alleviate the huge volumetric expansion of Ge upon lithiation, but also facilitates the transmission of lithium ions and electrons. Moreover, experiment analyses and density functional theory (DFT) calculations unveil the excellent lithium adsorption ability, high exchange current density, low activation energy for lithium diffusion of the hollow Ge@C electrode, thus exhibiting significant lithium storage advantages with a large charge capacity (1483 mAh/g under 200 mA g−1), distinguished rate ability (710 mAh/g under 8000 mA g−1) as well as long-term cycling stability (1130 mAh/g after 900 cycles under 1000 mA g−1). Therefore, this work offers new paths for controllable synthesis and fabrication of high-performance Ge based lithium storage nanomaterials.