This study characterizes the native oxide layer of Si nanoparticles and evaluates its effect on their performance for Li-ion batteries. x-ray photoelectron spectroscopy and transmission electron microscopy were applied to identify the chemical state and morphology of the native oxide layer. Elemental and thermogravimetric analysis were used to estimate the oxide content for the Si samples. Hydrofluoric acid was used to reduce the oxide layer. A correlation between etching time and oxide content was established. The initial electrochemical performances indicate that the reversible capacity of etched Si nanoparticles was enhanced significantly compared with that of the as-received Si sample.