We introduce a siloxane chain-based hydrophobizer that exhibits superior thermal and chemical stability compared to the conventional hydrophobizing silane agent under conditions of over 300 °C and pH 2-13. To demonstrate the capability of the siloxane chain-based hydrophobizer to serve as a highly robust chemical surface modifier, we present two applications: the formation of fine metal nanoparticles with a narrow size distribution by thermal aggregation of a metal thin film and the selective deposition of a ruthenium thin film by atomic layer deposition.