Natural rubber with filler nanomatrix structure was prepared by forming chemical linkages between natural rubber particles and filler nanoparticles. The filler nanomatrix structure was formed by graft copolymerization of vinyltriethoxysilane (VTES) onto natural rubber particles in the latex stage followed by casting of the latex to prepare an as-cast film. The silica nanoparticles were produced during the graft copolymerization through hydrolysis and condensation, i.e., sol-gel reaction; hence, they linked to the natural rubber particles. The nanomatrix structure was observed by transmission electron microscopy, in which the natural rubber particles of about 1 μm in diameter were well dispersed in the filler nanomatrix. Tensile properties were significantly improved by forming filler nanomatrix structure. The loss modulus and loss tangent of the natural rubber with the filler nanomatrix structure were almost independent of deformation frequency in the rubbery plateau region, which was explained to be due to the energetic elasticity and entropic elasticity characteristic of the nanomatrix structure.