Objective To summarize and analyze the clinical data of maple syrup urine disease (MSUD) patients to explore the correlation among clinical phenotype, biochemical markers and genotype. Methods The clinical data of 11 children with MSUD who were admitted to Guangzhou Women and Children’s Medical Center of Guangzhou Medical University between January 2011 and October 2016 were retrospectively collected. According to the clinical symptoms and prognosis, they were divided into classic type group (n=6) and intermediate/thiamine-effective group (n=5). The differences in biochemical metabolic markers between the two groups were compared, and the correlation between genotype and phenotype was analyzed. Results Compared to the intermediate/thiamine-effective group, the blood gamma-glutamyltransferase (γ-GT) level in the classic type group was significantly higher [158.00 (122.80, 309.30) vs. 11.00 (10.50, 14.00) U/L, P=0.004], and the globulin [(15.55±3.45) vs. (24.26±4.37) g/L, P=0.018] and lactate [1.05 (0.98, 1.68) vs. 2.10 (1.75, 2.70) mmol/L, P=0.030] levels in the classic type group were significantly lower, while the levels of alanine aminotransferase, aspartate aminotransferase and total bile acid were not different between the two groups (P>0.05). The plasma concentrations of leucine in the classic type group were higher than that in the intermediate/thiamine-effective group [(3748.20 (3135.00, 4936.00) vs. 620.40 (531.20, 1150.00) μmol/L, P=0.004]. The γ-GT level was positively correlated with the leucine level (rs=0.826, P=0.003), the leucine level was positively correlated with the iso-leucine level (rs=0.827, P=0.003), and the iso-leucine level was positively correlated with the valine level (rs=0.636, P=0.040). The results of gene sequencing showed that the 11 patients carried BCKDHA (n=4) and BCKDHB (n=7) gene mutations, respectively. Of these, 6 patients with BCKDHB gene mutations were classic type. Conclusion The prognosis of MSUD is closely correlated to blood γ-GT and branched-chain amino acids levels, as well as with genotype.