Silicon suboxide (SiO x ) has attracted widespread interest as Li-ion battery (LIB) anodes. However, its undesirable electronic conductivity and apparent volume effect during cycling impede its practical applications. Herein, sustainable rice husks (RHs)-derived SiO 2 are chosen as a feedstock to design SiO x /iron-nitrogen co-doped carbon (Fe-N-C) materials. Using a facile electrospray-carbonization strategy, SiO x nanoparticles (NPs) are encapsulated in the nitrogen-doped carbon (N-C) frameworks decorating atomically dispersed iron sites. Systematic characterizations including high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) and X-ray absorption fine structure (XAFS) verify the existence of Fe single atoms and typical coordination environment. Benefiting from its structural and compositional merits, the SiO x /Fe-N-C anode delivers significantly improved discharge capacity of 799.1 mAh g −1 , rate capability, and exceptional durability, compared with pure SiO 2 and SiO x /N-C, which has been revealed by the density functional theory (DFT) calculations. Additionally, the electrochemical tests and in situ X-ray diffraction (XRD) analysis reveal the oxidation of Li x Si phase and the storage mechanism. The synthetic strategy is universal for the design and synthesis of metal single atoms/clusters dispersed N-C frameworks encapsulated SiO x NPs. Meanwhile, this work provides impressive insights into developing various LIB anode materials suffering from inferior conductivity and huge volume fluctuations.