Chemisorbed molecular nanocorrals on semiconductor surfaces are of both fundamental and technical importance. 1-Propanethiol molecules adsorbed on Si(111)-(7×7) were investigated using high-resolution energy loss spectroscopy (HREELS), scanning tunneling microscopy (STM), and periodic density functional theory (DFT) calculations. HREELS spectra show that the 1-propanethiol molecules undergo S−H bond dissociative adsorption on Si(111)-(7×7). STM images reveal the temperature-dependent site selectivity for the binding of C 3 H 7 S-fragments. At room temperature, C 3 H 7 Sprefers to bind to faulted subunits compared to unfaulted subunits. At 110 K, C 3 H 7 S-binding on center adatoms over corner adatoms is dominant, resulting in an ordered array of molecular nanocorrals. DFT calculations were performed on a periodic slab including the entire 7×7 reconstruction rather than on a cluster model. The theoretical studies suggest that the temperaturedependent site selectivity originates from the thermal-plus-electron-induced diffusion of dissociative products and the sitepreferential accommodation of the mobile physisorbed precursors. Our results provide a fundamental understanding on the origin of site selectivity of molecular binding on Si(111)-(7×7).