Abstract We investigated the hierarchical structure of silica, especially agglomerate structure, in stretched rubber by time-resolved two-dimensional ultra-small-angle X-ray scattering (2D-USAXS). Time-resolved 2D-USAXS measurements give us the in-situ structural information up to 5 μm during sample deformation. The results are summarized as follows: at first, the agglomerate is turned so that the long axis of the agglomerate is parallel to the stretching direction, and the “weakly-bonded agglomerates” weakly bonding between agglomerates is broken down. Second, the distance between agglomerates increases with the small deformation of agglomerate. Finally, the “tightly-bonded agglomerates” strongly bonding between agglomerates start to deform. Existence of silane-coupling agents causes the differences in the manner of agglomerate deformation. These kinds of structural information will be a key to understanding the origin of rubber reinforcement by filler such as carbon black and silica.