Two-photon three-dimensional optical data storage is an effective method for high-capacity data storage. The beam of light passes through two different media (such as air and storage material)in writing three-dimensional information and influences the optical aberration and storage effect. So it is important for analysing the effect of each optical parameter of system on the optical aberration and storage impression of refractive index mismatch in the theory and experiment. First, the model of the optical storage system is set up， in the condition of the parallel flat and via wave aberration function deducing， the five primary Seidel aberrations: spherical aberration， coma， astigmatism， field curvature， and distortion， are gotten, and simulations and analyses on the primary aberration in the two case of horizontal and tilted storage material are performed. Simulation and experiment proved that the slope of optical aberration increased with the increase of storage depth; if numerical aperture got bigger optical aberration augmented quicklier.