Objective Based on the "gut-kidney axis" theory, to explore the molecular mechanism by which Bushang Tongluo Formula improves diabetic nephropathy (DN) in db/db mice. Methods Twelve-week-old db/db mice were treated with Buzang Tongluo Formula for 8 weeks, after which changes in renal function and renal pathology were assessed. Intestinal microbiota and renal metabolites in db/db mice were analyzed using second-generation Illumina sequencing and non-targeted metabolomics, respectively. Finally, protein immunoblotting was employed to verify the regulatory effects of Buzang Tongluo Formula on key proteins involved in renal carnitine metabolism (OCTN2, CPT1A) and fibrotic proteins (α-SMA). Results Compared with the normal control group, DN model mice showed significantly elevated serum creatinine (Scr), and 24-hour urinary total protein (24h-UTP) levels, along with obvious pathological kidney damage. Treatment with Bushang Tongluo Formula (especially the low dose) effectively reversed the above renal injury indicators. Metagenomic analysis revealed that conditionally pathogenic bacteria such as Lachnoclostridium, Faecalibacterium, Flavonifractor, and Blautia were enriched in the DN group, while probiotics such as Ligilactobacillus were depleted; Bushang Tongluo Formula significantly adjusted the abundance of these microbial communities. Metabolomics showed that Bushang Tongluo Formula could correct renal metabolic disorders, upregulate approximately 90% of differential metabolites, and significantly enrich pathways such as taurine metabolism. Integrated analysis indicated a strong negative correlation between carnitine and four bacterial taxa including Lachnoclostridium. Western blot confirmed that Bushang Tongluo Formula upregulated the expression of OCTN2 and CPT1A proteins in the kidneys of DN mice and downregulated α-SMA expression. Conclusion Bushang Tongluo Formula may alleviate renal fibrosis and improve DN-induced renal injury by regulating the intestinal microbiota and restoring renal carnitine metabolic homeostasis (upregulating OCTN2/CPT1A).