Atomic force microscopy probe-induced large-area ultrathin SiOx (x ≡ O/Si content ratio and x > 2) protrusions only a few nanometers high on a SiO2 layer were characterized by scanning photoemission microscopy (SPEM) and X-ray photoemission spectroscopy (XPS). SPEM images of the large-area ultrathin SiOx protrusions directly showed the surface chemical distribution and chemical state specifications. The peak intensity ratios of the XPS spectra of the large-area ultrathin SiOx protrusions provided the elemental quantification of the Si 2p core levels and Si oxidation states (such as the Si4+, Si3+, Si2+, and Si1+ species). The O/Si content ratio (x) was evidently determined by the height of the large-area ultrathin SiOx protrusions.