Three different Ti-Si oxide structuares, silica supported titania, silica coated titania and intimately mixed silicatitania, containing 10%-40% SiO2, were made by sol-gel process. The variations of microstructure parameters of nanocrystalline (nc) TiO2-anatase in the three kirds of binary oxides, including in-plane spacing d, cell constants (a0, CQ), cell volume V, cell axial ratio c0/a0 and crystal grain size, were comparatively investigated by high resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD). It is found that the microstructure parameters vary remarkably with increasing SiO2 content and annealing temperature. Different structured Ti-Si binary oxides lead to different variation tendencies of microstructure parameters. The more SiO2 the binary oxide contains, the more lattice defects of nc TiO2-anatase appear; diffusion or migration of Si cations could be an important influential factor in the variations of microstructure. The grain size of nc TiO2 in the three kinds of binary oxides not only depends on SiO2 content and annealing temperature but also on the degree of lattice microstrain and distortion of nc TiO2-anatase. Both grain size and phase transformation of nc TiO2-anatase are effectively inhibited with increasing SiOa content.