Objective The aim of this study was to explore the clinical manifestations, genetic copy number variations, therapeutic responses, and prognostic factors associated with 17p13.3 microdeletion syndrome in pediatric patients. Methods A retrospective analysis was conducted on the clinical profiles, whole exome sequencing data, and therapeutic outcomes of five pediatric cases diagnosed with 17p13.3 microdeletion syndrome. Results All 5 patients presented with short stature, and those in cases 3 to 5 also exhibited cardiovascular abnormalities. Whole exome sequencing identified a 433kb to 1536kb deletion within the 17p13.3 chromosomal region, predominantly affecting the YWHAE and CRK genes without implicating the PAFAH1B1 gene. Following the exclusion of contraindications, cases 1 to 4 were administered recombinant human growth hormone (rhGH). While the initial response to rhGH treatment was promising with improvements in height, the long-term efficacy was suboptimal. Cases 4 and 5 underwent surgical correction for congenital heart disease as indicated. Conclusion Deletion of 17p13.3 can result in 17p13.3 microdeletion syndrome. Whole exome sequencing is instrumental in the prompt diagnosis of children exhibiting signs of congenital heart disease and/or short stature. Timely and appropriate interventions for cardiovascular and height-related issues are essential for improving the overall prognosis of affected children.