Objective This study mainly analyzes the diagnostic value of two-dimensional ultrasonography (2D-US) combined with four-dimensional ultrasonography (4D-US) in prenatal ultrasound screening of fetal congenital malformations (CMs) and explores the high-risk factors affecting fetal malformations. Methods The clinical and imaging data of 2247 pregnant women who underwent prenatal fetal malformation screening in the General Hospital of Ningxia Medical University between February 2020 and October 2021 were collected and analyzed, retrospectively. All pregnant women underwent 2D-US, and those with suspected fetal malformations were further inspected by 4D-US. The accuracy of ultrasound examination results relative to actual pregnancy outcomes was analyzed, taking the neonatal malformation after induced labor or actual delivery as the gold standard, and the risk factors influencing the occurrence of fetal malformations were discussed. Results A total of 87 cases (3.87%) of fetal malformations were detected out of the 2247 parturients examined. The accuracy, sensitivity, and specificity of 2D-US diagnosis were 81.40%, 43.68%, and 82.92%, respectively, while the data were 83.67%, 51.72%, and 84.95% for 4D-US, respectively, and 93.59%, 90.80%, and 93.70%, respectively, for 2D-US +4D-US. The combined diagnosis of 2D-US +4D-US achieved statistically higher accuracy, sensitivity, and specificity than either of them alone. One-way analysis of variance and multivariate logistic regression analysis identified that the independent risk factors affecting fetal malformation were age ≥ 35, history of adverse pregnancy and childbirth, medication during pregnancy, toxic exposure during pregnancy, and history of seropositive for TORCH-IgM. Folic acid supplementation was a protective factor. Conclusions Prenatal US is an effective approach for screening fetal malformations. 2D-US +4D-US can effectively improve the diagnostic rate of fetal malformations. For pregnant women with high-risk factors, prevention should be given priority, and prenatal screening and prenatal diagnosis should be standardized to reduce the occurrence of fetal malformations.