A soft carbon and silicon suboxide modification strategy is presented to create homogeneous and multilayer core-shell structure silicon-based nanomaterials (Si@SiOx@C). The silicon suboxide layer thickness is homogeneous and can be effectively controlled from 2 to 15 nm through calcining the mesophase pitch-coated silicon nanoparticles at different temperatures. The optimized silicon suboxide thickness of 13.5 nm and a high graphitization degree of carbon allows for good protection of silicon nanoparticles. Correspondingly, quite good cycling performance with a specific capacity of 640 mAh g−1 and a superhigh coulombic efficiency of 99.4% is obtained for Si@SiOx@C anode after 700 cycles at a current of 0.2 A g−1. Si@SiOx@C also exhibits an excellent rate behavior with capacity retention of up to 70.3% when the discharge current increases from 0.05 to 20 A g−1. Such a novel and simultaneous growth of SiOx/carbon bilayers on Si nanoparticles will provide a facile synthesis strategy for the fabrication of high-performance silicon-based anode materials.