Confocal microscopy has high spatial resolution and signal to background ratio, possessing the capability of three-dimensional tomography of biological samples, and thus has been widely used in medicine and biology areas. Light in near-infrared II (NIR-II, 900-1 880 nm) regions fulfils moderate absorption, low scattering in biological tissues, and weak autofluorescence of biological tissues. Therefore, NIR-II in vivo fluorescence imaging has the advantages of large depth and high contrast. Point-excitation and point-detection based NIR-II confocal microscopy combines the advantages of the two technologies mentioned above and features high spatial resolution and high signal to background ratio in large-depth biological imaging. Therefore, it has been widely used in the biomedical fields. This review summarizes the principle and the development progress of NIR-II confocal microscopy and the application of biological imaging based on it. The future improvement and development directions of NIR-II confocal microscopy are also discussed.