Double network structure constructed with filler network of carbon black and molecular network of natural rubber possesses excellent toughness and strength. However, due to lack of proper in situ imaging techniques to detect the structural evolutions under loading, the reinforcement mechanism of filler network is still under debate. Here in situ synchrotron radiation X-ray nano-computed tomography with high spatial resolution (100 nm) is employed to study structural evolution of carbon black in a large volume of natural rubber matrix. For the first time, strain-induced deformation, destruction, and reconstruction of filler network are directly observed under cyclic loading. Combining mechanical test, the reinforcing and toughening effect of filler network is quantitatively assigned to three mechanisms, namely elastic deformation, destruction, and friction of filler network. Elastic deformation mainly occurs at low strain for energy storage, while network destruction plays the dominant role at larger strain to dissipate strain energy. Additionally, friction is another energy dissipation mainly at low strain.