Purpose: The purpose of this study was to investigate the pregnancy outcomes with a copper intrauterine device (IUD) in situ after 28 weeks of gestation and the association between pregnancy with copper IUDs and neonatal congenital malformations. Methods: This retrospective cohort study had compared the singleton pregnancies with the copper IUDs in situ and without IUDs after 28 gestational weeks in one delivery center of southeast China. The pregnant outcomes as preterm birth, premature rupture of membranes, infections and neonatal congenital malformations were observed and compared. The statistical analysis was carried out using R (version 4.0.4; R Development Core Team) statistical software. Results: A total of 147 pregnant women were included in our study, 73 with copper IUDs in situ were categorized into case group and 74 without IUDs during pregnancy into control group. In case group, the rates of premature rupture of membranes (38.36%) and spontaneous preterm birth (23.29%) were significantly high compared to control group. Women of elder age (≥35 years) in case group were more likely to experience premature rupture of membranes. The rates of neonatal congenital malformation were 10.96% (8/73) in case group and 1.35% (1/74) in control group respectively with no statistically significant difference. Conclusion: We had found that a copper IUD with pregnancy in situ increased the risk of premature rupture of membranes and spontaneous preterm birth after 28 gestation weeks, nearly one fourth of those women were encountered spontaneous preterm birth, but not increased risk of neonatal congenital malformations.