The invention discloses a probe-based confocal microendoscopy system and an adjusting method thereof. The probe-based confocal microendoscopy system comprises a laser device, an optical fiber circulator, a collimating lens group, a light beam scanning device, a relay leans group, a coupling object lens, an optical fiber beam probe, a photoelectric detector and a control unit. The optical fiber circulator is provided with three ports, the first port P1 receives exciting light, and the second port P2 outputs coupled exciting light and receives fluorescent light; the third port P3 outputs the fluorescent light; the control unit is used for controlling the laser device, the light beam scanning device and the photoelectric detector, processing signals detected by the photoelectric detector so as to generate images, calculating and outputting laser power target values to the laser device according to the detected signals and controlling the laser device to generate existing light according to the laser power target value to achieve automatic adjustment of input laser power. By means of the probe-based confocal microendoscopy system and the adjusting method thereof, the signal to noise ratio of the system is raised, and manufacturing cost is lowered; frequent manual operation of an operator is avoided, and operation can be simpler and more convenient.