Mesoporous silica thin films with different pore shapes were prepared by evaporation induced self-assembly method. The synchrotron radiation x-ray reflectivity and slow positron annihilation techniques were used to characterize the pore structures. The results indicated that with increase of the spin-coating speed, the pore structure transformed from 3-D cubic to 2-D hexagonal, the average porosity also decreased. The correlation of the film structures and positron annihilation parameters was songht for with FT-IR spectroscopy and isotropic inorganic pore contraction model.