Abstract: Cell autophagy， as a process of cell decomposition and metabolism， has a certain correlation with the physiological functions of spleen and stomach in traditional Chinese medicine (TCM) in maintaining the body's growth， development， immune defense and other functions. Based on the spleen and stomach theory， starting from the spleen-qi deficiency pathogenesis such as the body's transport disorder， insecurity of defense qi and the disorder of qi and blood supply and distribution， and combining with the research results of modern medicine on the decline of autophagy in cell metabolism， immune defense and aging， this paper analyzes the relationship between the spleen-qi deficiency pathogenesis and autophagy dysfunction， and puts forward that the decline of autophagy can be regarded as the microscopic pathogenesis of spleen-qi deficiency in TCM， and provides ideas for revealing the microscopic nature of spleen-qi deficiency.