Polyoxometalate (POM) presents great potential in oxidative desulfurization (ODS) reaction. However, the high dissolubility of POM in common solvents makes it difficult to recycle. Besides, the small specific surface area of POM also limits the interaction between them and the substrate. Depositing polyoxometalates onto three-dimensional (3D) network structured materials could largely expand the application of POM. Here, the surfaces of cellulose nanofibrils (CNFs) were modified with very few (3-Aminopropyl) trimethoxysilane (APTS) to endow positive charges on the surfaces of CNFs, and then phosphotungstic acid (PTA) was loaded to obtain the aerogel A-CNF/PTA as the ODS catalyst. FT-IR indicated the successful deposition of PTA onto aminosilane modified CNF surfaces. UV-VIS further suggested the stability of PTA in the aerogels. BET and SEM results suggested the increased specific surface area and the relatively uniform 3D network structure of the prepared aerogels. TGA analysis indicated that the thermal stability of the aerogel A-CNF/PTA50% was a little higher than that of the pure CNF aerogel. Most importantly, the aerogel A-CNF/PTA50% showed good catalytic performance for ODS. Catalysis results showed that the substrate conversion rate of the aerogel A-CNF/PTA50% reached 100% within 120 min at room temperature. Even after five cycles, the substrate conversion rate of the aerogel A-CNF/PTA50% still reached 91.2% during the dynamic catalytic process. This work provides a scalable and facile way to stably deposit POM onto 3D structured materials.