High-capacity silicon anodes suffer from rapid capacity decay due to large volume expansion, which causes mechanical fracture, electrical contact loss and unstable solid electrolyte interphase (SEI). Nanostructuring has proved to be effective in addressing these problems over the past decade; however, new issues such as poor initial Coulombic efficiencies due to increased surface area remain unsolved. Here we develop a surface-engineering strategy by depositing a dense silicon skin onto each mesoporous silicon microparticle and further encapsulating it with a conformal graphene cage, which improves both the initial and later-cycle Coulombic efficiencies. The silicon skin lowers the unfavorable electrolyte/electrode contact area and minimizes SEI formation, resulting in an initial Coulombic efficiency over twice as high as that without silicon skin coating. The graphene cage combined with the inner void space of mesoporous silicon allow for silicon expansion, which guarantees structural integrity and SEI stability, resulting in high later-cycle Coulombic efficiencies (99.8–100% for later cycles) and impressive cycling stability.