Silicon (Si) applied for lithium-ion battery anode is of immense prospect due to high theoretical capacity, non-toxic, abundant reserves and low-cost. But the electrode materials, maintaining stable structure during repeated discharge/charge processes, need to be explored, which can realize the long-life. To address this problem, we utilized hollow porous pollen carbon microsphere derived from biomass as hard template to accommodate nano-Si. The hollow porous carbon@nano-Si@graphene sheets (HPC@nano-Si@GS) microspheres with hollow double spherical interlayer and submicron porous structure have been successfully synthesized via a simple and green environment-protecting wet-chemical method. We decorate nano-Si with silane coupling agent which can bind hollow porous pollen and graphene oxide, realizing the strong fixation and protection of nano-Si. Furthermore, the surface submicron mesh pores and HPC microsphere provide enough buffer space to cushion the huge volume expansion for nano-Si, enhancing the cyclic stability. Finally, graphene wrapping on the surface of HPC@nano-Si@GS microspheres can protect nano-Si very well, further stabilizing the composite structure. Nano-Si particles were accommodated in the HPC microsphere with submicron pores and then coated by wrinkled graphene sheets, to form the strong structure with hollow double spherical interlayer. A series of electrochemical tests indicate that prepared HPC@nano-Si@GS microspheres with hollow porous carbon structure exhibit outstanding electrochemical properties.