For the compensation of the spherical aberration induced by refractive index mismatch in three-dimensional optical storage, the model of the optical storage is established, and the expression of the wavefront phase aberration function is achieved induced by refractive index with the storage depth. The phase aberration function is spred with Zernike polynomials. Under reading method of two-photon fluorescence and one-photon confocal fluorescence, the relation of the intensity with storage depth is obtained: under uncompensating the spherical aberration induced by refractive index mismatch, storage fluorescence intensity falls to zero in the storage depth of 200 μm; under compensating the first-order spherical aberration, the downtrend of storage fluorescence intensity with the storage depth is improved; under compensation the second-order spherical aberration, the storage fluorescence intensity varies little in the storage depth of 1 mm. And the method of the aberration compensation is analyzed in detail.