The development of advanced anode materials for lithium-ion batteries that can provide high specific capacity and stable cycle performance is of paramount importance. This study presents a novel approach for synthesizing molecular-level homogeneous carbon integration to porous SiO₂ nanoparticles (SiO₂@C NPs) tailored to enhance their electrochemical activities for lithium-ion battery anode. By varying the ratio of the precursors for sol-gel reaction of (phenyltrimethoxysilane (PTMS) and tetraethoxysilane (TEOS)), the carbon content and porosity within SiO₂@C NPs is precisely controlled. With a 4:6 PTMS and TEOS ratio, the SiO₂@C NPs exhibit a highly mesoporous structure with thin carbon and the partially reduced SiO_x phases, which balances ion and charge transfer for electrochemical activation of SiO₂@C NPs resulting remarkable capacity and cycle performance. This study offers a novel strategy for preparing affordable high capacity SiO₂-based advanced anode materials with enhanced electrochemical performances.