Near-infrared spectroscopy (NIRs) has been widely applied to rapid multi-component quality monitoring in the field of agriculture, pharmaceutical and food as a nondestructive testing method. Rapid and accurate detection of microbes is a challenging issue in clinical diagnosis, pharmaceutical and food processing technology. Biomacromolecules and water existing in cell walls, membranes and cells of microorganisms possess highly specific NIR spectra that can distinguish, identify and classify different microbes. In this paper, the research progress of NIRs in microorganism detection was reviewed by summarizing, sorting, analyzing and refining published literature. We first briefly introduced basic knowledge of microbiology and the fundamental NIRs for microbial detection. Then research progress at home and abroad of NIRs on microbe classification, foodborne microbial detection and microbial imaging detection was reviewed respectively. Finally, the existing problems and future application prospects of NIRs were also discussed to provide a reference for better use of NIRs in the field of microbial detection in the future.