Silicon is recognized as one of the most promising anode materials for lithium-ion batteries because of its extremely high theoretical capacity, low delithiation potential and abundant availability. However, Si experiences a huge volume expansion during lithiation and delithiation processes, which results in rapid capacity degradation and very poor cycling performance. Numerous studies have been conducted to circumvent these problems through the utilization of various silicon composite materials. Furthermore, suitable materials as well as proper design of nanostructures are a great challenge at this time. This review mainly focuses on the latest research achievements of Si composites and their nanostructures, including Si–carbon, Si–metal, Si–transition metal oxides and Si–polymer, which can improve the electrochemical performance of lithium-ion batteries effectively. In addition, the latest application of Si to other secondary batteries, such as sodium-ion batteries and magnesium-ion batteries is also included. Moreover, this review describes the remaining issues and future study directions.