The invention discloses a depth imaging super-resolution microscopic imaging system. The depth imaging super-resolution microscopic imaging system includes a first laser, a first lens, a first dichroscope, a second dichroscope, a second laser, a sixth lens, a phase modulation assembly, a third dichroscope, a deformation reflector, an X axis scanning vibrating mirror, a phase compensation assembly,a Y axis scanning vibrating mirror, a vertical optical path refraction matching unit, a second quarter wave-plate, a microscopic object lens, a sample table, a horizontal optical path refraction matching unit, a first optical filter, a wavefront sensor, a second optical filter, a tenth lens and an imaging device. By means of the two-photon effect, by compensating the fluorescent wavefront phase change through the wavefront sensor and the deformation reflector, by combining with movement of the sample table in the Z axis direction, the depth imaging super-resolution microscopic imaging systemcan realize three-dimensional depth imaging while correcting the aberration caused by the samples, thus being relatively higher in the imaging quality.