Aims/Background Prenatal diagnosis is a crucial tool in reducing birth defects. Research indicates that whole-exome sequencing (WES) is particularly effective for detecting abnormalities associated with structural ultrasound findings. This study aimed to evaluate the utility of WES in the genetic diagnosis of prenatal ultrasound abnormalities. Methods A total of 50 pregnant women with prenatal ultrasound abnormalities, diagnosed at Rizhao People’s Hospital between January 2023 and May 2024, were enrolled. Amniocytes, abortion tissues, and peripheral blood samples from the couples were collected for family-based WES. Results WES revealed genetic abnormalities in 20 out of 50 cases, resulting in a detection rate of 40%. The detection rates for specific abnormalities were as follows: skeletal abnormalities (41.7%), cardiovascular abnormalities (54.5%), central nervous system abnormalities (30%), urinary system abnormalities (50%), nuchal translucency thickening/hygroma colli (20%), and facial anomalies/cleft lip and palate (25%). The genetic detection rates for monosystemic and multisystemic abnormalities were 34.2% and 50%, respectively. Conclusion WES is crucial in the genetic diagnosis of prenatal ultrasound abnormalities, enhancing the accuracy of prenatal diagnostics and facilitating informed genetic counseling.