Abstract: Objective：To explore the general situation of fetal congenital malformations, and to investigate their risk factors. Methods：The clinical data of 558 pregnant and maternal women with congenital malformation fetuses in Huangpu Branch of Obstetrics and Gynecology Hospital Affiliated to Fudan University in 20142015 were descriptively analyzed, while 560 pregnant women who had delivered normal newborns were randomly selected into the control group. The univariate and multivariate unconditional logistic regression models were used to analyze the risk factors of fetal congenital malformations. Results：Of the 558 cases of congenital malformations, 397 cases were single system abnormality, and 161 cases were multisystem abnormality. The incidence of multiple malformation, skeletal system malformation, cardiovascular system malformation, nervous system malformation and urinary tract system malformation were among the highest. The main risk factors of congenital malformations were educational level (OR=2.355), maternal age ≥35 years (OR=13.945), pluriparity (OR=5.264), abnormal reproductive history (OR=23.491), mother’s emotion being nervous and melancholy (OR=6.929), passive smoking (OR=3.162), raising pets (OR=3.840), exposure to noise (OR=2.485), harmful chemical exposure (OR=5.700), pregnancy fever (OR=4.414), early viral infection (OR=6.603), taking drugs (OR=4.228), and anemia in gestational period (OR=26.402). The protective factors were folic acid (OR=0.056), calcium and iron (OR=0.115) supplements. Conclusions：The prevention of congenital malformations would be realized by reducing and controlling the dangerous factors in pregnancy, while improving eugenic counseling, screening, diagnosis and comprehensive evaluation.