Hyperspectral imaging (HSI) techniques play an important role in the food industry for providing rapid, nondestructive, and chemical‐free detection method, whereas a microscope can provide detailed information about the microstructure of a food item. As an emerging imaging spectroscopy technique, hyperspectral microscope imaging (HMI) technique combines the advantages of HSI with microscopic imaging and has been gradually applied in the food industry. This review introduces the principles of different kinds of HMI techniques, such as fluorescence HMI, visible/near‐infrared HMI, Raman HMI, and infrared HMI. Moreover, detailed applications of HMI techniques are summarized, including evaluation of structures of nutrients, and detection of microorganisms and residues. On the other hand, some challenges and future trends in the applications of these techniques are also discussed. It is concluded that by integrating HSI with microscopy, HMI can not only provide both spectral and spatial information about food substances but also provide their chemical information at the molecular or cellular level. Therefore, HMI techniques have great potentials in nondestructive evaluation of structures of nutrients, and detection of microorganisms and residues for the food industry.