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Abstract To observe the value of copy number variation sequencing（CNV-Seq）in the etiological diagnosis of fetal congenital heart disease. Methods： 80 pregnant women with fetal congenital heart disease (CHD）confirmed through echocardiography examined by 2 ultrasound doctors were included in this study. 30 ml amniotic fluid (during 16-24 gestational weeks）or 2 ml umbilical cord blood (more than 24 gestational weeks) of these women were transabdominal extracted under the guidance of ultrasound，and were detected by G-banding chromosome karyotype analysis and CNV-Seq. The positive detection rates of the two techniques were summarized and counted. Results：There were 8 women with abnormal fetal karyotypes in the 80 women with fetal CHD after karyotype analysis of fetus, with the detection rate of 10.0%, which included 4 cases with trisomy 21 syndrome of fetus, 3 cases with trisomy 18 syndrome of fetus, and 1 case with 46, XX, DER (6) (Q16Q22) of fetus, and the results of which was consistent with the results of CNV-Seq detection. In 72 fetuses after karyotype analysis, there were 10 cases with pathogenic copy number variation of fetal chromosome, with the detection rate of 13.8%, and there was 1 case with 1 unknown clinical copy number variation, with the detection rate of 1.4%. Conclusion：CNV-Seq can not only detect the conventional chromosome number and structural abnormalities of fetal CHD，but also can detect the microdeletion and microduplication information of chromosome fragment，which can increase the diagnostic value and can provide the evidences for genetics counseling.
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