Fetal skeletal dysplasia is a disease that is difficult to distinguish these types of diseases during the fetal period. Due to the difficulty of fetal ultrasound diagnosis, the severity of fetal skeletal dysplasia is extremely difficult to assess. For this condition, we analyzed 79 fetal samples of skeletal dysplasia from the third affiliated hospital of Zhengzhou University, China from August 2018 to April 2020, which had undergone prenatal whole exome sequencing(WES). By comparing the results of whole-exome sequencing and fetal ultrasound test results, we find that the fetal short limb phenotype found in the range of FL<-4.0SD or HL<-4.0SD through ultrasound test is closely related to FGFR3 gene mutation , and the correlation is stronger when accompanied by macrocephaly. We also find that the fetal limb curved phenotype is closely related to COL1A1 gene mutation. At the same time, we find that nasal dysplasia during fetal period is also a common phenotype of abnormal results detected by whole exome sequencing. Overall, our research shows that WES has different detection rates for various skeletal abnormalities according to the different types of ultrasound detection results, which provides a meaningful guidance for clinical diagnosis of fetal skeletal dysplasia.