The strategies, misconceptions, technical methods and preferred protocols of cell autophagy research, as well as the regulatory mechanism of autophagy in non-alcoholic fatty liver disease (NAFLD) are discussed. At the same time, the current status of research on autophagy mechanism in TCM treatment of NAFLD is discussed. Autophagy is believed to protect hepatocytes in pathogenesis (mainly the early stage) and treatment of NAFLD, and to some extent delay the development of the disease. The protective effect of autophagy may also be reflected in the micro-effect mechanism of traditional Chinese medicine in the treatment of potential diseases by “preventing development and transmission of diseases”. Autophagy is currently in the ascendant in the research of mechanism of Chinese medicine intervention in diseases and has broad research prospects. However, there are still research bottlenecks. Based on the staged achievements in the standardization of traditional Chinese medicine, it is possible to speed up the autophagy research in traditional Chinese medicine by developing new in-vitro techniques, combined with high-throughput bioinformation collection and cutting-edge bioanalytical techniques.