Silicon anodes deliver batteries with energy densities much higher than those based on today’s dominant graphite anodes. However, they commonly exhibit huge volume variations and unfavorable interface stability, causing a gradually diminishing capacity on extended cycling. Most Si-based batteries consisting Si/C composites in industry can only use a very limited amount of Si (<30 % by weight). Exploiting molecular layer deposition (MLD) technique, a fluorine-rich flexible inorganic–organic hybrid alucone (AlFHQ) shell is controllably deposited onto Si electrodes. Employing ex situ XPS and AFM, the AlFHQ film presents reversible electrochemical evolutions in terms of composition and morphology. The interactions the between Li+ and −O−2,3,5,6-fluorobenzene functional groups help to construct a mechanically-chemically robust LiF-rich hybrid solid electrolyte interphase (SEI) on Si anode, delivering enhanced interfacial stability and integrity of electrode. An optimized coating thickness (≈5 nm) for interfacial stabilization and Li+ transport kinetics is demonstrated, namely, Si@AlFHQ-20. The reported fluorine-rich hybrid modification technique endows (a), stable cycling of Si anode (≈3.8 mAh cm−2) with an ultrahigh initial Coulombic efficiency (ICE) of 92.3 %; (b), enhanced rate capability of 1468 mAh/g at 2.0 A g−1 and good cycling performance; and (c), overall cell (Si@AlFHQ-20//LiCoO2@Al2O3) operational stability for more than 100 cycles under stringent cathode conditions (2.68 mAh cm−2, high cutoff voltage at 4.55 V).