Various kinds of efforts have been devoted to ameliorate the serious volume-expansion effect and low electron conductivity of silicon-based materials in lithium ion batteries. Here, we report a facile high voltage sputtering process to prepare three-dimensional hierarchical porous nitrogen-doped carbon coated Si microsphere to significantly improve the lithium storage performance. The structure and morphology of the as-obtained samples are characterized by X-ray diffraction, transmission electron microscope and scanning electron microscope. The results indicate that the as-prepared composite is composed of silicon nanoparticles (similar to 100 nm) coated with conductive thin carbon layer (similar to 8.5 nm). The composite shows excellent lithium storage performance with a reversible capacity of 1565 mAh g(-1) after 100 cycles at a current density of 0.5 A g(-1), as well as a long cycling performance at the high current density of 2 A g(-1). The facile preparation process and highly silicon-loading (similar to 78%) makes the prepared material be a great potential application in lithium-ion batteries.