A novel method was used to prepare a magnetic phenylene-based periodic mesoporous organosilica nanocomposite with yolk–shell structure (Fe₃O₄@YSPMO). The Fe₃O₄@YSPMO nanomaterial was prepared by using easily accessible pluronic-P123 and cetyltrimethylammonium bromide (CTAB) surfactants under basic conditions. This material was employed for effective immobilization of potassium perruthenate to prepare an Fe₃O₄@YSPMO@Ru nanocatalyst for the aerobic oxidation of alcohols. The physiochemical properties of the designed Fe₃O₄@YSPMO@Ru nanocomposite were studied using PXRD, FT-IR, TGA, SEM, TEM, ICP, VSM and XPS analyses. Fe₃O₄@YSPMO@Ru was effectively employed as a highly recoverable nanocatalyst in the selective aerobic oxidation of alcohols.