The gut microbiota, comprising trillions of microorganisms, plays a crucial role in maintaining host health and homeostasis through complex metabolic interactions. This review explores the intricate relationships between gut microbiota-derived metabolites and their impact on various physiological processes, including metabolism, mucosal integrity, and communication among gut tissues. Key metabolites such as short-chain fatty acids (SCFAs), intermediate bile acid (BA) metabolites, amino acid-derived metabolites, and membrane-associated lipids are discussed, highlighting their mechanisms of action and therapeutic potential. The review also delves into the interplay between gut microbiota and other organs, such as the bone marrow, lungs, liver, and pancreas, emphasizing the dynamic and multifaceted nature of these interactions. Understanding these interactions is essential for developing innovative strategies to promote well-being and improve outcomes in chronic diseases. The future holds promise for personalized therapies, advanced metabolomics, and microbiome engineering to harness the therapeutic potential of gut microbiota-derived metabolites.The gut microbiota, comprising trillions of microorganisms, plays a crucial role in maintaining host health and homeostasis through complex metabolic interactions. This review explores the intricate relationships between gut microbiota-derived metabolites and their impact on various physiological processes, including metabolism, mucosal integrity, and communication among gut tissues. Key metabolites such as short-chain fatty acids (SCFAs), intermediate bile acid (BA) metabolites, amino acid-derived metabolites, and membrane-associated lipids are discussed, highlighting their mechanisms of action and therapeutic potential. The review also delves into the interplay between gut microbiota and other organs, such as the bone marrow, lungs, liver, and pancreas, emphasizing the dynamic and multifaceted nature of these interactions. Understanding these interactions is essential for developing innovative strategies to promote well-being and improve outcomes in chronic diseases. The future holds promise for personalized therapies, advanced metabolomics, and microbiome engineering to harness the therapeutic potential of gut microbiota-derived metabolites.