The rapid development of alternative energy vehicles has raised higher requirements for electrode materials. Silicon, with superhigh specific capacity, is highly anticipated in the field of lithium‐ion batteries (LIBs). Unfortunately, the original drawbacks of serious volumetric effect and poor conductivity have confined its commercial steps severely. Herein, a novel composite, based on submicron silicon flakes embedded into carbon shell, with heterojunction‐bearing MnOx nanoparticles, is designed and synthesized successfully via sanding process and in situ thermal reduction methods. The results of electrochemical performance tests and related fitting data show that the presence of MnOx particles facilitates rapid Li+ transport and reduces the impedance associated with Li+ diffusion from the surface to the inner core of the MnOx/Si@C material. The two‐dimensional (2D) silicon flakes and uniform carbon shell have positive influence on structural stability and electronic conductivity. Benefit from the rational design, the optimized MnOx/Si@C composite delivers an outstanding cycling stability of 1106.59 mAh·g−1 at 1 A·g−1 over 1000 cycles with a capacity retention of 71.09%. Besides, the goal material possesses a lithium‐ion diffusion coefficient of ≈1.04×10−9 cm2·s−1. This work provides a reference for the mass preparation of advanced anode materials for lithium‐ion batteries.