Birth defects, as a kind of diseases that seriously affect human life, have always attracted much attention. In the past, perinatal data have been studied for birth defects. This study analyzed the surveillance data of birth defects during the perinatal period and the whole of pregnancy, as well as the independent influencing factors, to help to minimize their risk of birth defects. A total of 23,649 fetuses delivered in the hospital from January 2017 to December 2020, were enrolled in this study. There were 485 cases of birth defects, including live births and stillbirths by detailed inclusion and exclusion criteria. Maternal and neonatal clinical data were collated to analyze the influencing factors associated with birth defects. Pregnancy complications and comorbidities were diagnosed according to the criteria of the Chinese Medical Association. Univariate and multivariate logistic regression models were used to investigate the association between independent variables and birth defect events. The incidence of birth defects during the whole of pregnancy was 175.46/10,000, while the incidence of perinatal birth defects was 96.22/10,000. The birth defect group had significantly higher maternal age, gravidity, parity, rate of preterm birth, cesarean section (CS) rate, scarred uterus, stillborn, and male newborns compared to the control group. Multivariate logistic regression model analysis showed that preterm birth [odds ratio (OR): 1.69, 95% confidence interval (CI): 1.01 to 2.86], CS (OR: 1.46, 95% CI: 1.08 to 1.98), scarred uterus (OR: 1.70, 95% CI: 1.01 to 2.85), and low birth weight (OR >4 compared to the other two classes) were significantly associated with birth defects during the whole of pregnancy (all P<0.05). The independent influencing factors associated with perinatal birth defects included CS (OR: 1.43, 95% CI: 1.05 to 1.93), gestational hypertension (OR: 1.70, 95%: 1.04 to 2.78), and low birth weight (OR >3.70 compared to the other two classes). The discovery and monitoring of known influencing factors associated with birth defects, such as, preterm birth, gestational hypertension, low birth weight, should be enhanced. For the controllable influencing factors, obstetrics providers should work with patients to minimize their risk of birth defects.