The invention provides a nano silicon dioxide with grafting of polyisoprene on the surface, a preparation method and an application thereof. The preparation method comprises the steps of dispersing the nano silicon dioxide in a solvent, then adding an RAFT (Reversible Addition Fragmentation chain Transfer) reagent with carboxyl groups, a dewatering agent and a catalyst for reaction to obtain nano silicon dioxide capable of initiating RAFT polymerization of isoprene monomers; then mixing with the isoprene monomers for reaction to obtain the nano silicon dioxide with grafting of the polyisoprene on the surface. The nano silicon dioxide particles can improve the blending effect of different rubbers or the rubbers and plastic molecules in a more-effective manner by utilizing the compatibility of the grafted polyisoprene and a base material so as to provide a better basis for exerting the synergistic property of different components in a more-effective manner.