The internal dispersion structure of silica fillers in polymer matrix is significant for design and fabricating high-performance polymer composite. In order to explore the relationship between fillers spatial dispersion states and mechanical properties, we use superficial fluorescent labeling to achieve fillers visualization in polymer matrix with laser scanning confocal microscopy. Through the effect of fluorescent silane coupling agent, the uniform red fluorescence characteristics were shown on the silica surface. The 2D-planar and 3D-spatial dispersion states of silica fillers in rubber matrix can be accurately observed with fluorescence imaging technology. The results by Avizo software statistics show that high-content silica fillers in composite tend to undergo dissociation of aggregates. These dissociated small volume aggregates which facilitate the interaction between particles and rubber matrix to dissipate mechanical energy effectively and rapidly improve rubber toughness. This successful visualization method opens a new avenue in spatial dispersion description of fillers aggregates in organic-inorganic composite.