Objective To explore the potential of serum miR-126 as a new biomarker in congenital heart disease (CHD) clinical application and evaluation. Methods 40 children with acyanotic CHD (ACHD group) including 15 children with heart failure (ACHD I) and 25 children without heart failure (ACHD II), 14 age matched children with cyanotic CHD (CCHD group) and 20 healthy children (control group) were enrolled in this study. Real-time PCR was used to quantify the serum miR-126 expression level in 54 patients’ serum samples and 20 healthy controls, and the relationship of their expression and clinic pathological features were analyzed. Results Compared with normal controls, the expression levels of miR-126 in ACHD group and CCHD group were significantly downregulated (P < 0.001). The expression levels of miR-126 in CCHD group were significantly lower than that in ACHD group (p < 0.001). miR-126 expression levels were lower in ACHD I than in ACHD II (p < 0.001). Conclusion The expression levels of serum miR-126 were closely correlated with the severity and the degree of impaired cardiac function, indicating the potential of miR-126 as a new biomarker for the congenital heart disease.