Alloy anodes, particularly silicon, have been intensively pursued as one of the most promising anode materials for the next generation lithium-ion battery primarily because of high specific capacity (>4000 mAh/g) and elemental abundance. In the past decade, various nanostructures with porosity or void space designs have been demonstrated to be effective to accommodate large volume expansion (∼300%) and to provide stable solid electrolyte interphase (SEI) during electrochemical cycling. However, how to produce these building blocks with precise morphology control at large scale and low cost remains a challenge. In addition, most of nanostructured silicon suffers from poor Coulombic efficiency due to a large surface area and Li ion trapping at the surface coating. Here we demonstrate a unique nanoperforation process, combining modified ball milling, annealing, and acid treating, to produce porous Si with precise and continuous porosity control (from 17% to 70%), directly from low cost metallurgical silicon source (99% purity, ∼ $1/kg). The produced porous Si coated with graphene by simple ball milling can deliver a reversible specific capacity of 1250 mAh/g over 1000 cycles at the rate of 1C, with Coulombic efficiency of first cycle over 89.5%. The porous networks also provide efficient ion and electron pathways and therefore enable excellent rate performance of 880 mAh/g at the rate of 5C. Being able to produce particles with precise porosity control through scalable processes from low-grade materials, it is expected that this nanoperforation may play a role in the next generation lithium ion battery anodes, as well as many other potential applications such as optoelectronics and thermoelectrics.