To address the significant challenges encountered by silicon‐based anodes in high‐performance lithium‐ion batteries (LIBs), including poor cycling stability, low initial coulombic efficiency (ICE), and insufficient interface compatibility, this work innovatively prepares high‐performance Si/SiOx@F‐C composites via in situ coating fluorine‐doping carbon layer on Si/SiOx surface through high‐temperature pyrolysis. The Si/SiOx@F‐C electrodes exhibit superior LIB performance with a high ICE of 79%, exceeding the 71% and 43% demonstrated by Si/SiOx@C and Si/SiOx, respectively. These electrodes also show excellent rate performance, maintaining a capacity of 603 mAhg−1 even under a high current density of 5000 mAg−1. Notably, the Si/SiOx@F‐C electrode sustains a high reversible capacity of 829 mAh g−1 at 1000 mA g−1 over 1400 cycles, and 588 mAhg−1 at 3000 mAg−1 even over 2400 cycles, capacity retention of up to 82.12%. Comprehensive characterization and analysis of the fluorine‐doped carbon layer reveal its role in enhancing electrical conductivity and preventing structural degradation of the material. The abundant fluorine in the coating layer significantly increases the LiF concentration in the solid electrolyte interface (SEI) film, improving interfacial compatibility and overall lithium storage performance. This method is both straightforward and effective, providing a promising blueprint for the broader application of Si‐based anodes in advanced lithium batteries.