Silicon has been considered as one of the most promising high-capacity anode materials because of its environmentally friendly character, natural abundance, and attractive operating voltage. However, successful implementation of Si-based anodes in Li-ion batteries is seriously hindered by their huge volume variation and low electric conductivity. The rational design of Si and effective combination of nanosized Si with carbonaceous materials represent the most effective approaches to overcome the challenges towards practical application of Si-based anodes. In this review, the mechanisms of Li–Si alloying and cell failure are briefly analyzed to comprehend the inherent impediments of Si-based anodes. Furthermore, nano-structured Si materials are summarized and nano/micro-structured Si/C and SiO_x/C composites with 3D conductive networks and stable interfaces are discussed in detail. Accessory battery components that influence electrochemical performance are also reviewed. As for practical application, full batteries with Si-based anodes are discussed. Finally, the key aspects of Si-based materials are emphasized and prospective strategies for promoting the practical applications of Si-based anodes in high energy density Li-ion batteries are proposed.