Metabolism affects or is influenced by almost every other biological activity. With the deepening of medical research, understanding the nature of natural metabolism is the primary means to solve complicated diseases. Therefore, starting from metabolism, starting from the root, starting from the pathophysiological basis, and realizing the transformation from the underlying mechanism to clinical medicine will be the way that the scientific research community must go for a long time in the future. This review mainly discusses that metabolites produced by some major metabolic pathways, such as glucose metabolism, lipid metabolism, and amino acid metabolism, are important signal transmitters and regulators of activity. It expounds on the role of metabolism in various system diseases, including cardiovascular system diseases, nervous system diseases, endocrine system diseases, and intestinal microbial system diseases, from the levels of metabolites, proteins, organelles, tissues, and systemic physiology.