SiO/Graphite (Gr) composite has been regarded as one of the most promising anode materials for the next generation of high-energy-density lithium-ion batteries (LIBs). The heterogeneous composition of such an anode system brings in highly nonlinear and complex electrochemical behaviors compared to the single-material anode. The computational modeling provides an efficient and accurate way to explore the electrochemical behaviors of SiO/Gr composite anode. Herein, we propose a 3D model at the electrode level containing particle geometries based on a representative volume element (RVE) and study the electrochemical process of the half-cell charging. The effects of SiO proportion, charging rate, SiO distribution, and SiO particle size on the electrochemical performance are discussed. The results reveal that an anode with higher SiO proportions performs a better rate capability. We also discover that moving SiO particles towards the separator and shrinking the SiO particle can improve the cell performance. Results provide an in-depth understanding of the electrochemical behaviors of the composite anode and guide the design for SiO/Gr anode materials in maximizing the theoretical capacity while maintaining better rate performance.