To examine whether maternal hair or cord blood selenium levels are associated with infant congenital heart defects (CHDs).A hospital-based case-control study was performed with samples collected from 2010 to 2014. Selenium levels in maternal hair and fetal cord serum were measured using Inductively Coupled Plasma-Mass Spectrometry (ICP-MS). Data from medical records of infants with congenital heart defects were collected. Logistic regression analysis was employed to examine the independent association between maternal selenium exposure and fetal CHD.In total, 888 pregnant women were included in this study. Median (inter-quartile range) selenium levels in of maternal hair was similar in the control and CHD group. A significant association was detected between increased maternal hair selenium concentration and CHDs in offspring (aOR 3.57, 95 %CI: 1.90-6.70). The association was present in all CHD groups, including septal defects, conotruncal defects, left ventricular outflow tract obstruction, right ventricular outflow tract obstruction, and anomalous pulmonary venous return.High maternal selenium level is significantly associated with the occurrence of fetal CHD.