The invention discloses a near-infrared laser scanning confocal imaging system, which comprises a light path scanning unit and a control unit which adopt a confocal structure, wherein the light path scanning unit comprises a near-infrared laser source, a collimation and extension module, a laser optical filter, a dichroic reflector, a scanning galvanometer, an f-theta lens, a tube lens, an imaging objective lens, a fluorescent optical filter, a convergent lens, a pinhole, a detector and the like, the control unit comprises a motion control module used for controlling the scanning galvanometer, a data acquisition module used for acquiring an output signal of the detector, a data processing module connected with the motion control module and the data acquisition module, and the like. The method matched with the system is characterized in that a sample is marked with near-infrared quantum dots with the fluorescence emission spectrums between 932nm and 1250nm, and then the sample is detected by the near-infrared laser scanning confocal imaging system. According to the system disclosed by the invention, deep-level imaging of samples such as biological tissues can be accurately and efficiently realized, and the system has a simple structure and is easy to operate.