The invention discloses a small structured light illumination super-resolution microscopic imaging system which includes a laser light source, a collimating lens, a rotary light baffle module, a dichroic mirror, a filter plate, a microscopic objective lens, a carrier table, an imaging lens, a photoelectric detector and a synchronous control system. The light emitted by the laser light source is collimated by the collimating lens into parallel beams, the parallel beams are partially blocked by the rotary light baffle module, divided by the dichroic sheet and filtered by the filter plate placedon the entrance pupil surface of the microscopic objective lens, and then, structured light illumination is formed on the surface of a sample on the carrier table through the microscopic objective lens. The imaging lens and the photoelectric detector are placed behind the dichroic mirror and used for forming an image of fluorescence distribution on the surface of the sample. The synchronous control system is connected in a control manner with the rotary light baffle module, the carrier table and the photoelectric detector. The small structured light illumination super-resolution microscopic imaging system has the advantages of small size, compact structure, low cost, and the like, and is easy to carry. The application scope of structured light illumination super-resolution imaging is greatly extended.