The Imaging theory of two-photon and multi-photon confocal scanning microscopy is presented. The three-dimensional point spread function and three-dimensional optical transfer function of two-photon confocal scanning microscopy is derived. By using the three-dimensional point spread function and three-dimensional optical transfer function theory, we have proved that the horizontal and vertical resolutions of two-photon confocal scanning microscopy are higher than those of the single photon confocal scanning microscopy, and the space resolution of multi-photon confocal scanning microscopy is higher than that of two-photon confocal scanning microscopy.