Residual Si was produced on a furnace wall when upgraded metallurgical grade Si was refined by electron beam melting. It was then recycled to prepare Si-SiOx nanoparticles with an average size of 100 nm by planetary ball milling. The obtained Si-SiOx nanoparticles mainly consist of amorphous Si, crystalline Si and amorphous SiOx, which was confirmed by XRD, FTIR, XPS and TEM. SiOx is mainly composed of SiO2 and SiO1.35. Distilled water used as a grinding aid not only enhances milling efficiency, but also plays a key role in obtaining SiOx. During refining of upgraded metallurgical grade Si, the deposition pattern of residual Si on furnace wall agrees with model of three-dimension growth. Growth of Si-SiOx nanoparticles is the mutual effect of distilled water and ball milling. Si-SiOx nanoparticles were doped into phenolic resin pyrolysis carbon as anode materials for lithium ion batteries, and 10% doping was observed to improve the specific capacity. After 500 cycles, specific capacity of delithiation remained around 550 mA h/g. It suggests the residual Si is a value-added by-product, and it can be recycled as anode materials for lithium ion batteries.