A three-channel fluorescence localization super-resolution biological microscope system, comprising an objective lens, an imaging lens, an illumination module and an imaging module; wherein the illumination module is used to realize three channels, wide-field and semi-total internal reflection illumination and total internal reflection illumination, and is adjustable in an illumination mode; illumination light generated by the illumination module is reflected by a first multicolor reflector to illuminate a sample through the objective lens; characterized in that the three-channel fluorescence localization super-resolution biological microscope system further comprises a three-dimensional nanoscale sample locking module; fluorescent light emitted from the sample is allocated by an allocation light splitter after passing through the first multicolor reflector and a front imaging lens, one part is allocated into the three-dimensional nanoscale sample locking module, and the other part is allocated into the imaging module; the three-dimensional nanoscale sample locking module is arranged to lock the position of the sample in the ultrahigh image photographing process; the imaging module is arranged to allocate different bands of fluorescent light generated by a first channel, a second channel and a third channel into three different optical paths, and the fluorescent light of the three channels is imaged onto different positions of a detector chip; the three-dimensional nanoscale sample locking module adopts a light emitting diode different from the three-channel illumination light source as a light-field light source to illuminate the sample through a Kohler illumination optical path; after passing through a microscope main body, one part is imaged on a locking camera, and a fourth filter is arranged between the allocation reflector and the locking camera; the three-dimensional nanoscale sample locking module utilizes a light emitting diode different from the three-channel illumination light source to provide the light-field illumination to the sample through the Kohler illumination optical path; the light received by the objective lens from the sample is allocated by the allocation light splitter, and one part of the light is imaged on the locking camera through the front imaging lens; the locking camera is connected with a computer; when a program of the computer is started, the program is arranged to capture a real-time image from the locking camera, and the program is arranged to calculate a local contrast of the image in real time and select an optimum area so as to adopt the area having a maximum sum of the local contrast as a position of an optimum area; the three-dimensional nanoscale sample locking module also comprises a piezoelectric ceramic platform, and when the locking is begun, the locking program is arranged to control the piezoelectric ceramic platform through a piezoelectric ceramic platform drive to scan up and down on a longitudinal focal plane; during the scanning, a calibration image sequence is captured from the locking camera, and a corresponding z value is recorded; the locking program is arranged to intercept a fixed-sized area from the uppermost or lowermost image of the calibration image sequence at the position of the optimum area as a reference image; a spatial correlation matrix is solved for the sequence image and the reference image, and Gaussian fitting is performed for the spatial correlation matrix; a monotone decrease correspondence between a fitting peak value and the z value is solved, and a multi-time function is used for approximate fitting; subsequently, the locking program is arranged to capture a light-field image of the sample in real time from the locking camera; a spatial correlation matrix is solved for a real-time image and the reference image, and is subjected to Gaussian fitting; a solved center position is used as an offset on the XY plane, and a real-time z value is solved by fitting the limit value; and the locking program is arranged to drive the piezoelectric ceramic platform to compensate the offset through a drive circuit.