Tissue optical clearing technique combined with two-photon microscopy (TPM) can improve the imaging depth of biological samples. However, the refractive index mismatch between objective medium and optical clearing agent will cause spherical aberration which degrades the fluorescence intensity and axial resolution. To solve this problem, we analyzed the effect of SA at the focus, and built a spherical aberration compensation model based on objective characteristics (numerical aperture and immersion media), the imaging depth and the sample refractive index. Then, we corrected the spherical aberration by incorporating a spatial light modulator into the TPM system. The TPM images of fluorescent bead phantom and optical clearing brain tissues show considerable improvement of fluorescence intensity and axial resolution. The proposed correction process is simple and fast since it does not require repeated imaging. More importantly, it is suitable for different objectives and optical clearing agents.