Adding silica nanofiller in silicone rubber can toughen the matrix 3 orders in terms of fracture energy, which is far larger than most other nanofiller–rubber systems. To unveil the astonishing toughening mechanism, we employ in situ synchrotron radiation X-ray nanocomputed tomography (Nano-CT) technique with high spatial resolution (64 nm) to study the structural evolution of silica nanofiller in silicone rubber matrix at different strains. The imaging results show that silica nanofiller forms three-dimensional connected network, which couples with silicone chain network to construct a double-network structure. Stress-induced phase separation between silica nanofiller and silicone polymer chain networks is observed during tensile deformation. Unexpectedly, though the spatial position and morphology of nanofiller network changes greatly at large strains, the connectivity of nanofiller network shows negligible reduction. This indicates that nanofiller network undergoes destruction and reconstruction simultaneously, during which silica nanofiller serves as reversible high functionality cross-linker. The reversible bonding between silica nanofiller and silicone rubber or between nanofiller particles can dissipate mechanical energy effectively, which may account for the 3 orders enhancement of toughness.