Objective To investigate the clinical phenotype and genetic variant characteristics of children with Shwachman-Diamond syndrome (SDS). Methods From January 2018 to September 2023, seven children with SDS under long-term follow-up in the Department of Pediatric Endocrine and Genetics were selected as the research objects. The clinical data of children were gathered and peripheral blood samples were collected for exome sequencing (ES), and lineage validation of the variants was performed by Sanger sequencing. Results Among the 7 children with SDS, 3 were boys and 4 were girls. The median age at first diagnosis was 3.0 (0.9-4.0) years. Six patients carried SBDS defects and one case carried EFL1 defect. Among the six patients with SBDS deficiency, five of them carried compound heterozygous variants (two cases with the variants of c.258+2T>C/c.183_184delinsCT, one case with c.258+2T>C/c.40A>G, one case with c.258+2T>C/c.184A>T, one case with c.258+2T>C/ heterozygous deletion of exon 3), and the remaining one patient carried SBDS homozygous variation (c.258+2T>C). Patients with SBDS deficiency were initially diagnosed with short stature (6/6, 100%), and combined with chronic diarrhea (3/6, 50%) and recurrent respiratory infections (1/6, 16.7%). Through examination, all the six patients with SBDS deficiency (100%) were found to have neutropenia and elevated liver enzymes. Four cases had skeletal dysplasia and 3 cases had exocrine pancreatic dysfunction. One SDS patient was confirmed to carry compound heterozygous variants of EFL1 (c.2260C>T/c.316G>A). The main clinical manifestations included short stature and abnormal skeletal development, without pancreatic and blood system involvement. Conclusions Children with SBDS deficiency presented clinical phenotypic heterogeneity. The phenotypic spectrum and variation spectrum of SDS in China were enriched, and an SDS patient with EFL1 variant was reported for the first time in the Chinese population. For children with short stature and symptoms such as neutropenia, exocrine pancreatic dysfunction, and skeletal deformities, genetic testing should be completed to avoid missing the diagnosis of SDS.