Objective To screen mutations in 3′UTR region of NOTCH2 gene of children with tetralogy of Fallot disease (TOF) and explore possible mechanisms that how mutations in this region affect the expression of NOTCH2 gene. Methods One hundred and fifty-two children confirmed with TOF were selected as subjects (TOF group), and another 107 healthy children were chosen as controls (CON group). PCR was employed to amplify 3′UTR region of NOTCH2 gene. Direct forward and reverse sequencing was performed on the PCR products. The sequence of 3′UTR region of NOTCH2 gene was compared with the known sequence (NG_008163.1) in GenBank by the BLAST program and possible mutations were screened. Online software PicTar and TargetScan were used to predict miRNA which could bind to 3′UTR region of NOTCH2 gene. The effects of mutations in 3′UTR region of NOTCH2 gene on the expression of miRNA-regulated NOTCH2 gene were analyzed. Results A new mutation and 5 reported SNPs in 3′UTR region of NOTCH2 gene, i.e. 2 672(157020T>G), rs368873082(156595C>T), rs835576(156691A>G), rs3795664(156937C>T), rs699779(156967T>C), and rs699780(156836T>C) were detected. The differences of the frequencies of alleles of 5 reported SNPs of the TOF group and CON group were not statistically significant (P>0.05). Results of prediction showed that there were 34 miRNAs that might bind to 3′UTR region of NOTCH2 gene and this mutation did not locate in binding regions of 34 miRNAs and 3′UTR region of NOTCH2 gene. Conclusion A new mutation 157020T>G exists in 3′UTR region of NOTCH2 gene. This mutation may affect the binding efficiency of miRNA and 3′UTR region of NOTCH2 gene by spatial configuration changes, and further affect the normal expression of NOTCH2 gene. Five SNPs in 3′UTR region of NOTCH2 gene are not significantly correlated with the susceptibility of TOF.