The conceptual design of yolk-shell structured Si/C composites is considered to be an effective way to improve the recyclability and conductivity of Si-based anode materials. Herein, a new type of yolk-shell structured Si/C composite (denoted as TSC-PDA-B) has been intelligently designed by rational engineering and precise control. In the novel structure, the multiple Si nanoparticles with small size are successfully encapsulated into the porous carbon shells with double layers benefiting from the strong etching effect of HF. The TSC-PDA-B product prepared is evaluated as anode materials for lithium-ion batteries (LIBs). The TSC-PDA-B product exhibits an excellent lithium storage performance with a high initial capacity of 2108 mAh g−1 at a current density of 100 mA g−1 and superior cycling performance of 1113 mAh g−1 over 200 cycles. The enhancement of lithium storage performance may be attributed to the construction of hybrid structure including small Si nanoparticles, high surface area, and double carbon shells, which can not only increase electrical conductivity and intimate electrical contact with Si nanoparticles, but also provide built-in buffer voids for Si nanoparticles to expand freely without damaging the carbon layer. The present findings can provide some scientific insights into the design and the application of advanced Si-based anode materials in energy storage fields.