The influence of soft interphase on molecular aggregation states and mechanical properties of block copolymer-grafted silica nanoparticles composites was investigated in this study. Rubbery poly(butyl acrylate) (PBA) and glassy poly (methyl methacrylate) (PMMA) were chosen as the inner and outer layers, respectively, which were prepared by 2-steps atom-transfer radical-polymerization (ATRP). Variation of ordered structure of silica particles under mechanical deformation were investigated by in-situ ultra small-angle X-ray scattering (USAXS). The hybrid films became more rubber-like after incorporating rubbery PBA between silica and PMMA. The structural colors exhibited in the film due to the photonic crystal-like ordered structure. An ordered arrangement of particles was observed in local regions by atomic force microscope (AFM). Fourier transform of AFM images revealed that the colloidal particles form a paracrystalline ordering. In the USAXS profile, the experimental data fit to the theoretical function of face-centered cubic (FCC) structure. While elongation, the distance of [111] plane increased along the elongation direction increased, and decreased along the direction perpendicular to elongation. The compressive strain of [111] plane in the direction perpendicular to elongation were varied among samples with different weight ratios of hard/soft blocks, indicating the change of Poisson’s ratios in different samples.