Octavinyl polyhedral oligomeric silsesquioxane (POSS) was polymerized on the surface of Fe3O4 nanoparticles (NPs) and then the NPs were functionalized with carboxylic acid groups using thiol-ene click reactions with thioglycolic acid. The as-prepared Fe3O4@POSS-COOH magnetic hybrid NPs had mesoporous structures with an average particle diameter of 15 nm and a relatively high specific surface area of 447 m2·g−1. Experimental results showed that 4 mg of Fe3O4@POSS-COOH NPs efficiently adsorbed and removed methylene blue from water at 5 min. This is due to the presence of both carboxylic acid and pendant vinyl groups on the Fe3O4@POSS-COOH NPs. These NPs could be easily withdrawn from water within a few seconds under moderate magnetic field and showed high stability in acid and alkaline aqueous mediums.