The ability to quantifiably characterize the structure of mesoporous membranes over a large sample surface area is inherently crucial to the preparation of well-controlled and functional mesoporous silica films. To estimate the degree of ordering in silica films on a statistical level, grazing incidence small angle x-ray scattering (GISAXS) was used to analyze the nanostructure of silica films with high-ordered mesochannel arrays, and a general analysis model was developed for interpreting the resulting GISAXS patterns. Structural information on the films, including the mesochannel size, orientation, positional distribution factor, subunit number in coherent region, and mesochannel length distribution, were obtained by fitting the model to the experimental data. The GISAXS analysis results showed the gradually decreasing ordering of silica film, which can be attributed to two aspects: the positional deviation from ideal lattice sites in the plane perpendicular to the substrate surface, and the wide length distribution of the mesochannels. The proposed model is expected to be successfully extendable to the analysis of several other types of mesoporous film with different pore morphologies.