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Investigating the internal factors that affect the initial coulombic efficiency (ICE) of silicon/graphite (Si/G) composites and improving ICE are critical to promote applications of Si/G composites in lithium-ion batteries. Here, four types of Si/G composites are prepared with different specific surface area, Si–G phase interface and charge transfer impedance (Rct) to study the internal factors affecting the ICE of Si/G composites. The experimental results show that the influencing factors on ICE of Si/G composites are not only specific surface area, but also the Si–G phase interface and Rct. During the first lithiation process of Si/G composites, there are some reversible phase (LixSi, LixC) and irreversible phase (Li2O, Li2SiO4 and organolithium) formed, the ICE of Si/G composites is mainly determined by the irreversible phase. The specific surface area, Rct and Si–G phase interface can affect the reaction kinetics of the materials and the ratio of reversible/irreversible phase content, which ultimately affect the ICE of Si/G composites. A smaller specific surface area and well Si–G phase interface with a low Rct will bring a higher ICE of Si/G composites. This report may provide a new idea for the research of ICE of Si/G composites and promote their practical application.