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To investigate the causal effects of plasma metabolites on the progression and recovery of Achilles tendon injury (ATI), Mendelian randomization (MR) was applied using a two-sample approach with genetic data from two large datasets. ATI data were sourced from the IEU-OpenGWAS project (ebi-a-GCST90018895), while plasma metabolite data included 1,400 metabolites. Significant instrumental variables (IVs) for metabolites were identified, and five MR methods-IVW, MR-Egger, weighted median, simple mode, and weighted mode-were applied to assess causal relationships. Reverse MR analysis was conducted to explore the impact of ATI on metabolite levels. Tissue repair and the expression of IL-6, TNF-α, VEGFA, and TGF-β1 in mouse Achilles tendon tissue were assessed on day 7 post-treatment with 5,6-dihydrothymine (Dih) and hydroxyasparagine (Hyd) using H&E staining and Western blot. MR analysis identified 19 metabolites with significant causal associations to ATI. Of these, 12 metabolites, including Dih (IVW: OR = 1.197, 95% CI: 1.074-1.334; P = 0.001) and Pregnanediol-3-glucuronide (IVW: OR = 1.098, 95% CI: 1.023-1.177; P = 0.001), were positively associated with ATI progression. In contrast, 7 metabolites, such as Hyd (IVW: OR = 0.789, 95% CI: 0.707-0.880; P < 0.001), were linked to ATI recovery. Reverse MR analysis did not indicate significant causal effects of ATI on metabolite levels, suggesting a unidirectional relationship. X-ray and H&E analyses revealed that Dih and Hyd treatment significantly enhanced Achilles tendon healing in a dose-dependent manner. Further, Dih and Hyd treatment notably reduced IL-6 and TNF-α expression (P < 0.05) while increasing VEGFA and TGF-β levels (P < 0.05), indicating a reduction in inflammation and promotion of tissue repair. This study identified potential causal relationships between specific plasma metabolites and ATI outcomes. These findings may inform future therapeutic strategies and highlight the utility of MR in exploring metabolite-disease associations.