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The objective of this study is to investigate the therapeutic effects of Shengqing Jiangzhuo (SQJZ) Capsules on chronic renal failure (CRF) by examining their influence on intestinal microbiota and metabolomic profiles. SQJZ's active ingredients were identified using UPLC-Q-Exactive-Orbitrap-MS. A chronic renal failure model was induced in rats via 16 weeks of intragastric adenine administration, followed by 35 days of daily treatment. Blood samples were analyzed for UA, BUN, Scr, Cys C, TNF-α, and IL-6. Kidney tissue underwent Hematoxylin and Eosin (HE) staining, Masson's Trichrome staining, and immunohistochemical analysis to assess histopathological changes, as well as alterations in macrophage and neutrophil populations. Immunohistochemistry evaluated renal inflammatory and fibrotic proteins (NLRP3, caspase-1, TGF-β1, fibronectin, and collagen I). RT-qPCR measured mRNA levels of IL-1β, TNF-α, and IL-6, while immunofluorescence staining evaluated intestinal tight junction proteins (Occludin, Claudin-1, ZO-1). Gut microbiota changes were analyzed via 16S rRNA gene sequencing, serum metabolites through untargeted metabolomics, and Spearman correlation assessed links between microbial taxa and metabolites. Rats in the model group showed significantly higher levels of UA, BUN, Cys C, Scr, TNF-α, and IL-6, along with reduced body weight, compared to the control group (P < 0.001). Treatment with SQJZ Capsules at various doses significantly lowered these levels and improved body weight (P < 0.001). HE staining revealed renal fibrosis and inflammation, with increased mesangial cell proliferation and collagen deposition in the model group (P < 0.01). Intestinal tissues showed increased thickness, reduced villi, and fewer goblet cells. SQJZ Capsules at high, medium, and low doses significantly improved renal structural damage compared to the model group. This was shown by reduced mesangial cell and matrix proliferation, less glomerular injury, decreased inflammatory cell infiltration, and reduced fibrosis. Intestinal villus structure was restored, inflammatory cells decreased, goblet cell numbers increased, and mucosal thickness was reduced. Masson's trichrome staining revealed significant collagen deposition and severe renal fibrosis in the model group versus the control group (P < 0.01). Immunohistochemical analysis showed a significant rise in macrophages and monocytes in the kidneys of model group rats compared to controls. SQJZ Capsule treatment notably reduced these inflammatory cells, with the high-dose group showing the most significant effects (P < 0.01). All treatment groups showed a significant reduction in collagen deposition and renal fibrosis (P < 0.01), with the high-dose group showing the most improvement. Immunohistochemistry revealed that SQJZ Capsules reduced renal expression of NLRP3, caspase-1, TGF-β1, fibronectin, collagen I, IL-1β, TNF-α, and IL-6, with the strongest effects in the high-dose group. Immunofluorescence confirmed increased Occludin, Claudin-1, and ZO-1 expression, especially in the high-dose group. SQJZ Capsules also normalized gut microbiota, particularly Erysipelatoclostridium and Lactobacillus levels. Untargeted metabolomics found 530 differential metabolites, mainly affecting phenylalanine, α-linolenic acid, ascorbate and aldarate, tryptophan, and arachidonic acid pathways. These findings suggest that SQJZ Capsules may offer a multi-target therapeutic strategy for CRF by modulating the gut microbiota and associated metabolic pathways. SQJZ Capsules enhanced renal function and reduced fibrosis, likely by modulating gut microbiota and metabolism, thereby decreasing inflammation and renal damage in CRF.