Silicon as an electrode suffers from short cycling life, as well as unsatisfactory rate-capability caused by the large volume expansion (~400%) and the consequent structural degradation during lithiation/delithiation processes. Here, we have engineered unique void-containing mesoporous carbon-encapsulated commercial silicon nanoparticles (NPs) in yolk-shell structures. In this design, the silicon NPs yolk are wrapped into open and accessible mesoporous carbon shells, the void space between yolk and shell provides enough room for Si expansion, meanwhile, the porosity of carbon shell enables fast transport of Li+ ions between electrolyte and silicon. Our ex-situ characterization clearly reveals for the first time that a favorable homogeneous and compact solid electrolyte interphase (SEI) film is formed along the mesoporous carbon shells. As a result, such yolk-shell Si@mesoporous-carbon nanoparticles with a large void exhibits long cycling stability (78.6% capacity retention as long as 400 cycles), and superior rate-capability (62.3% capacity retention at a very high current density of 8.4Ag−1).