Objective：To summarize the genotypic and phenotypic characteristics of patients with short stature based on the clinic feature and second-generation sequencing technology. Methods：Patients met the criteria of short stature were included in study who visited the Department of Endocrinology and Genetic Metabolism，Children’s Hospital of Chongqing Medical University from May 2015 to May 2020. The phenotypes of the patients were collected and the genotypes of patients were analyzed by second-generation sequencing technology. Results：The study included 175 patients，of which 81 were found pathogenic or likely pathogenic gene mutations，with a detection rate of 46.29%；there were 46 single gene mutations，10 copy number variations，2 gene imprinting abnor－malities and 1 chromosome abnormality；29 unreported mutation sites were found. The gene diagnosis rate of patients with syndromic short stature was higher in this cohort，and the patients with short stature，accompanied with bone X-ray abnormality，bone deformity，special face，sexual development disorder and stunting were more likely to have genetic etiology. Conclusion：The second-generation sequencing technology is helpful to clarify the genetic etiology of patients with short stature and expand clinicians’ understanding of genotype and phenotype of patients with short stature at molecular level.