The severe volumetric expansion of silicon nanoparticles (~400 %) limits their practical application as an anode material for next-generation lithium–ion battery (LIB). Here, we describe the fabrication and characterization of conformal polydopamine carbon shell encapsulating rattle-type silica@silicon nanoparticles (PDA−PEI@PVP−SiO2@Si) with tunable void structure prepared following a dual SiO2 template using (3–aminopropyl)triethoxysilane (APTES) as a self-catalytic, structure-directing agent to tetraethyl orthosilicate (TEOS) pretreated with polyvinylpyrrolidone (PVP K30) via modified Stöber process. Polyethylene imine (PEI) crosslinking facilitated the construction of interconnected three-dimensional bubble wrap-like carbon matrix structure through hydrothermal treatment, pyrolysis, and subsequent surface-protected etching. The composite anode material delivered 539 mAh·g−1 capacity after 100 cycles at 0.1 A·g−1, and 453 mAh·g−1 rate performance at 5 A·g−1. The satisfactory electrochemical performance of the PDA−PEI@PVP−SiO2@Si was attributed to the following: the rattle-type structure providing void space for Si volume expansion, PVP K30-pretreated APTES/TEOS SiO2 seeds via catalyst-free, hydrothermal-assisted Stöber protecting Si/C spheres upon etching, carbon coating strategy increasing Si conductivity while stabilizing the solid electrolyte interface (SEI), and PEI carbon crosslinks providing continuous conductive pathways across the electrode structure. The present work realizes a promising strategy to synthesize the tunable yolk–shell C@void@Si composite anode materials for high power/energy-density LIB applications.