At 17(+4) week, non-invasive prenatal testing (NIPT) results of a 24-years-old mother showed high risk of monosomy X (45, X). Abnormally shaped head and cardiac defects were observed in prenatal ultrasound scan at 19(+3) week. Amniocentesis conducted at 19(+3) week identified karyotype 47, XX, +18, which suggested that the NIPT failed to detect trisomy 18 (T18) in this case. With a further massively parallel sequencing (MPS) of maternal blood, fetal and placental tissues, we found a confined placental mosaicism (CPM) with non-mosaic T18 fetus and multiclonal placenta with high prevalence of 45, X and low level of T18 cells. FISH and SNP-array evidence from the placental tissue confirmed genetic discrepancy between the fetus and placenta. Because the primary source of the fetal cell-free DNA that NIPT assesses is mostly originated from trophoblast cells, the level of T18 placental mosaicism may cause false negative NIPT result in this rare case of double aneuploidy.