Vacuum ultraviolet (VUV, λ = 172 nm) irradiation of alkyl self-assembled monolayers (SAMs) in the presence of dry air alters their surface properties. In this work, UV photochemically prepared hexadecyl (HD)-SAMs on hydrogen-terminated silicon substrates were irradiated by VUV light in dry air, which generated active oxygen species upon excitation of the atmospheric oxygen molecules. These active oxygen species converted the terminal methyl groups of the SAMs to polar functional groups, which were examined quantitatively by X-ray photoelectron spectroscopy (XPS) and chemical labeling. At the first stage of VUV irradiation, the surface of SAMs was functionalized, and the ratios of the generated polar functional groups markedly increased. With the elongation of the irradiation period, the SAMs gradually degraded, and the total polar group percentages gradually decreased. The difference between the oxygenated carbon components derived by the deconvolution of the XPS carbon (C1s) spectrum and the chemical labeling of polar groups revealed enormous quantities of ethereal and ester groups that cannot react with the labeling reagents but are included in the C1s spectral envelope. These modifications were reflected on morphological structures of SAMs, which were gradually distorted until a complete amorphous structure was obtained after the complete elimination of HD-SAMs.