To explore the value of non-invasive prenatal testing (NIPT) for the detection of fetal chromosome copy number variations (CNVs). Clinical data of 18 661 pregnant women who underwent NIPT were collected. For fetuses suspected for carrying CNVs, amniotic fluid samples were collected for chromosomal karyotyping and/or chromosomal microarray analysis (CMA). Among all samples, NIPT suggested that 58 fetuses carried trisomy 21, 18 carried trisomy 18, 19 carried trisomy 13, 1 carried trisomies 18 and 21. Eighty eight women accepted invasive prenatal diagnosis. The results of CMA in 59 cases were consistent with those of NIPT, which yielded a consistency rate of 67.05%. In addition, 37 cases of fetal CNVs were detected by NIPT, of which 19 (15 microdeletions and 4 microduplications) have accepted invasive prenatal diagnosis. In 14 cases, the results were consistency with those of NIPT, with a consistent rate of 73.68%. NIPT features high sensitivity and accuracy. Invasive prenatal diagnosis should be considered for CNVs detected by NIPT, and by tracing its parental origin, it can provide guidance for clinical practice.