Porous structured silicon (p-Si) has been recognized as one of the most promising anodes for Li-ion batteries. However, many available methods to synthesize p-Si are difficult to scale up due to their high production cost. Here we introduce a new approach to obtain spherical micrometer-sized silicon with unique porous structure by using a microemulsion of the cost-effective of silica nanoparticles and magnesiothermic reduction method. The spherical micron-sized p-Si particles prepared by this approach consist of highly aligned nano-sized silicon and exhibit a tap density close to that of bulk Si particles. They have demonstrated significantly improved electrochemical stability compared to nano-Si. Well controlled void space and a highly graphitic carbon coating on the p-Si particles enable good stability of the structure and low overall resistance, thus resulting in a Si-based anode with high capacity (~1467 mAh g−1 at 2.6 A g−1), enhanced cycle life (370 cycles with 83% capacity retention), and high rate capability (~650 mAh g−1 at 11A g−1). This approach may also be generalized to prepare other hierarchical structured high capacity anode materials for constructing high energy density lithium ion batteries.