Food quality and safety are the essential hot issues of social concern. In recent years, there has been a growing demand for real-time food information, and non-destructive testing is gradually replacing traditional manual sensory testing and chemical analysis methods with lagging and destructive effects and has strong potential for application in the food supply chain. With the maturity and development of computer science and spectroscopic techniques, machine learning and hyperspectral imaging (HSI) have been widely demonstrated as efficient detection techniques that can be applied to rapidly evaluate sensory characteristics and quality attributes of food products nondestructively and efficiently. This paper first briefly described the basic concepts of hyperspectral imaging and machine learning, including the imaging process of HSI, the type of algorithms contained in machine learning, and the data processing flow. Secondly, this paper provided an objective and comprehensive overview of the current applications of machine learning and HSI in the food supply chain for sorting, packaging, transportation, storage, and sales, based on the state-of-art literature from 2017 to 2022. Finally, the potential of the technology is further discussed to provide optimized ideas for practical application.