In this paper, as an example of the structural analysis of silica filler in rubbers by synchrotron small angle X-ray scattering, we show the application to end-modified styrene butadiene rubber (SBR) for fuel-efficient tire. The distribution of particle size of silica aggregates can be obtained by the analysis of scattering profile, and it is shown that radius of silica aggregate is smaller and distribution of particle size is narrower in end-modified SBR than in non-modified SBR. Deformation behavior of silica aggregates during elongation reveals to be different between modified and non-modified SBR by the simultaneous ultra-small angle X-ray scattering and stress-strain curve measurement. We have found the difference of mechanism of stress-strain curve between modified and non-modified SBR by the computer simulation using the results of ultra-small angle X-ray scattering experiment.