Spherical graphite (SG) is a kind of primary anode material for lithium-ion batteries (LIBs), but the charge–discharge rate of SG are not fast enough to adapt to the increasing battery demand. At higher charge and discharge rates, the sluggish kinetics of lithium-ion insertion and extraction negatively impacts the rate performance and cycle stability of the battery. Herein, the micro-expansion treatment and carbon coating are combined to prepare micro-expanded graphite material with nitrogen-doped amorphous carbon layers (PCN@MEG). The micro-expansion treatment opens the graphite and increases the interlayer spacing, maintaining the overall spherical morphology of the graphite. These optimizations reduce lithium-ion diffusion resistance and accelerates the insertion/extraction process. The nitrogen-doped carbon coating improves the initial coulombic efficiency (ICE) and forms a protective barrier on the graphite surface. The ICE of PCN@MEG increased to 75.47% (compared to 70.73% for micro-expanded graphite). The PCN@MEG exhibits a high capacity of 212.37 mAh g−1 at 3C. After 500 cycles at 1C, the capacity retention is 95.33%. After 500 cycles at 3C rate, the capacity retention is 79.15%.