The invention discloses a 3D multi-focal-plane structured illumination quick microscopic imaging system and method. The system is composed of an objective lens OL, a delay lens group, a diffraction multi-focal grating MFG, an aberration correction grating CCG, a digital microlens array DMD, a first 4f group, a second 4f group, and an imaging module. The delay lens group is used for enabling lightwith different depths to arrive at a light-sensitive surface of a camera after passing through a multi-focal grating. The aberration correction grating CCG is used for eliminating an aberration of a corresponding sub graph of a sample at a same depth. The digital microlens array is used for modulating illumination patterns of the sample at different depths. The first 4f group is used for realizingmatching of the size of a laser beam with the size of the digital microlens array DMD; and the second 4f module is used for matching of the size of the pattern on the digital microlens array DMD withthe size of the diffraction multi-focal grating MFG. And the imaging module is used for collecting data, carrying out structured illumination super-resolution microscopic reconstruction on the sampleat different depths, and stacking the reconstruction results of all layers to form a final 3D super-resolution imaging result. Therefore, the speed of microscopic imaging is increased effectively andthe stability of the system is improved.