Objective To explore the application value of single nucleotide polymorphism (SNP) microarray in the prenatal diagnosis of fetal congenital heart disease. Methods A total of 200 pregnant women and fetuses were selected for prenatal diagnosis due to fetal congenital heart disease and/or positive ultrasound soft indicators. Chromosome karyotype and SNP array analysis were performed in amniotic fluid cells to analyze the detection rate of the two techniques and to determine the nature of copy number variation. Results Only 1 case of chromosome abnormality was detected by common karyotype, and 22 cases were detected by SNP array technique, among which 11 cases were pathogenic copy number variation (CNVs) and 11 cases were CNVs with unclear clinical significance. Conclusions SNP technology can significantly increase the detection rate, and has important application value for fetuses with congenital heart disease with normal karyotypes.