This meta-analysis aimed to comprehensively assess the teratogenic risk to offspring associated with continuing pregnancy after administering mifepristone and/or misoprostol during gestation. We conducted a systematic search of multiple databases, including PubMed, Web of Science, Embase, Cochrane, CNKI, and CBM, from their inception to February 2024, with no language restrictions. We included cohort and case-control studies that analyzed the teratogenic effects of mifepristone and/or misoprostol on fetuses and newborns. Quality assessment was performed using the Newcastle-Ottawa Scale (NOS). The odds ratios (OR) from individual studies were combined using meta-analysis. Sensitivity testing and heterogeneity analysis were conducted. A total of 13 studies were eligible for inclusion, comprising 5193 cases of congenital malformations and 12,232 controls. Our findings indicated that the use of misoprostol during early pregnancy increased the risk of congenital abnormalities in offspring (OR = 2.69; 95% CI: 1.57-4.62). However, the potential teratogenic effect of mifepristone during pregnancy cannot be ruled out. Additionally, the use of mifepristone and/or misoprostol has been linked to a higher risk of certain congenital anomalies, such as hydrocephalus (OR = 3.41; 95% CI: 1.17-9.97), Möbius syndrome (OR = 26.48; 95% CI: 11.30-62.01), and terminal transverse limb defects (OR = 10.75; 95% CI: 3.93-29.41). (PROSPERO, CRD42024522093, 03182024).