Background: Mitochondrial short-chain enoyl-CoA hydratase 1 deficiency (ECHS1D) is an inborn metabolic disorder caused by biallelic variants in the ECHS1 gene. Although five urinary metabolites—SCPCM, SCPC, SCECM, SCEC and 2,3DH2MB—were identified at the time of the initial disease report, their diagnostic utility and relationship with disease severity are not well established. Methods: We conducted a retrospective study of 73 patients with genetically confirmed Leigh syndrome, including 38 with ECHS1D (case group) and 35 with other genetic causes (control group). Diagnostic performance of each metabolite was evaluated using receiver operatingcharacteristic curves. A multivariate logistic regression was conducted to construct a diagnostic prediction model. Results: According to the current laboratory’s cut-off value, urinary 2,3DH2MB and SCPCM both exhibited high sensitivity (92.1%), but the specificity of 2,3DH2MB was only 28.5%. In contrast,urinary SCPCM and SCPC showed high specificity , with SCPC reaching 90%. ROC analysisrevealed that SCPC had the highest diagnostic efficacy (AUC = 0.902), followed by SCPCM,SCECM, and 2,3DH2MB. Urinary SCEC showed no diagnostic value. The final prediction model, incorporating SCPC, SCPCM, and SCECM, achieved an AUC of 0.964 (95% CI: 0.917–1.000), with good calibration and clinical utility . Except for SCEC, elevated levels of 2,3DH2MB, SCPCM, SCPC, and SCECM were significantly correlated with greater disease severity . Conclusion: Urinary SCPC, SCPCM, and SCECM serve as valuable diagnostic biomarkers for ECHS1D, and their combined application optimizes diagnostic performance. We recommend incorporating these metabolites into routine metabolic screening for LS.