This study investigated expression of serum miR-27b and miR-451 in patients with congenital heart disease associated pulmonary arterial hypertension (CHD-PAH), and analyzed the risk factors of CHD-PAH. A total of 114 patients with CHD admitted to the First Affiliated Hospital of the University of South China were recruited and allocated into a study group (61 patients with PAH) and a control group (53 patients without PAH). Reverse transcription-polymerase chain reaction (RT-PCR) was employed for the qualification of serum miR-27b and miR-451, and an automatic biochemical analyzer was used for the measurement of biochemical indexes in peripheral blood, and enzyme-linked immunosorbent assay (ELISA) for the detection of serum brain natriuretic peptide (BNP) and asymmetric dimethylarginine (ADMA). The patients with CHD-PAH showed higher serum miR-27b, BNP and ADMA but lower miR-451 than the controls. Serum miR-27b was positively correlated with mean pulmonary artery pressure (mPAP), BNP and ADMA, whereas serum miR-451 was negatively correlated with them. The combined detection of miR-27b and miR-451 was more valuable than a single detection in the diagnosis of CHD-PAH. Logistic regression analysis showed that ADMA, miR-27b, miR-451 and ventricular septal defect (VSD) were independent risk factors for CHD-PAH. In conclusion, miR-27b is highly expressed and miR-451 and the expression is low in patients with CHD-PAH. miR-27b and miR-451 are significantly correlated with BNP, ADMA, and the severity of the disease. The combination of miR-27b and miR-451 has high diagnostic value and can be used as a biomarker for the diagnosis and assessment of CHD-PAH. CHD-PAH is common in children with CHD, which poses a serious threat to the life and safety. At present, there are no effective methods for its early diagnosis and treatment. MicroRNAs (miRNAs, miRs) have been found to be closely related to the pathogenesis of CHD-PAH. In this study, miR-27b and miR-451 with differential expression in CHD-PAH were evaluated, and it was found that they were of great significance in the diagnosis and assessment of CHD-PAH.