The invention discloses a super-resolution microscopy method and system based on saturated pumping-stimulated emission detection and belongs to fields of super-resolution microscopy imaging and nonlinear optics. The system comprises a light source module, a detection module and a processing module, wherein a sample is put between the light source module and the detection module, the light source module comprises a first light source emitting excitation light, a second light source emitting reading light, a modulation device, a dichroscope and a galvanometer scanner, the detection module comprises a photo detector, the photo detector is connected with a lock-in amplifier, and the lock-in amplifier is in communicated connection with the processing module. On the basis of confocal microscopy,saturated excitation light is introduced and is limited in time domain, so that the sample can be entangled with a fluorescent high-order harmonic signal; in addition, another beam of reading laser is introduced, so that to-be-emitted fluorescence is emitted in a form of stimulated emission light, finally, a high-order harmonic signal of the stimulated emission light is demodulated through phase-locked detection, so as to obtain a final imaging result.