Bile acids (BAs) have evolved from their traditional role as auxiliary molecules in lipid digestion to critical signaling molecules regulating host metabolism. In recent years, the role of microbiota-derived bile acid-modifying enzymes and their mediated novel bile acid metabolic pathways in the pathogenesis and progression of metabolic diseases has become increasingly prominent. These microbial enzymes fine-tune glucose and lipid metabolism, energy homeostasis, and inflammatory responses by modulating the composition and proportion of the bile acid pool, thereby influencing the activity of key receptors such as the farnesoid X receptor (FXR) and the G protein-coupled bile acid receptor (TGR5). The theory of "harmonizing the liver and spleen" in traditional Chinese medicine (TCM) is closely related to the maintenance of homeostasis of the liver-spleen axis. TCM posits that "liver Qi failing to ensure free flow" (liver dysfunction) and "spleen failing to transport and transform" (spleen dysfunction) are the core pathogenesis of metabolic diseases, while modern research has confirmed their intrinsic pathophysiological links to bile acid metabolic disorders and gut microbiota dysbiosis. Studies have shown that TCM formulations and active ingredients based on the "harmonizing the liver and spleen" principle can effectively ameliorate metabolic disorders such as insulin resistance and lipid accumulation by targeted intervention of microbiota-derived bile acid-modifying enzymes, regulating downstream receptor signaling pathways like FXR and TGR5, consequently correcting bile acid metabolic abnormalities and remodeling the gut microbiota structure. This review systematically summarizes the key targets of the microbiota-derived bile acid-receptor axis in metabolic diseases and delves into the intervention mechanisms of "harmonizing the liver and spleen" TCM strategies based on this axis, aiming to provide a new scientific explanation and potential therapeutic strategies for the prevention and treatment of metabolic diseases with TCM.