(1) Background: Optical genome mapping (OGM) is a novel approach to identifying genomic structural variations with high accuracy and resolution. We report a proband with severe short stature caused by 46, XY, der (16) ins (16;15) (q23; q21.3q14) that was detected by OGM combined with other tests and review the clinical features of patients with duplication within 15q14q21.3; (2) Methods: OGM, whole exon sequencing (WES), copy number variation sequencing (CNV-seq), and karyotyping were used; (3) Results: The proband was a 10.7-year-old boy with a complaint of severe short stature (−3.41SDS) and abnormal gait. He had growth hormone deficiency, lumbar lordosis, and epiphyseal dysplasia of both femurs. WES and CNV-seq showed a 17.27 Mb duplication of chromosome 15, and there was an insertion in chromosome 16 found by karyotyping. Furthermore, OGM revealed that duplication of 15q14q21.3 was inversely inserted into 16q23.1, resulting in two fusion genes. A total of fourteen patients carried the duplication of 15q14q21.3, with thirteen previously reported and one from our center, 42.9% of which were de novo. In addition, neurologic symptoms (71.4%,10/14) were the most common phenotypes; (4) Conclusions: OGM combined with other genetic methods can reveal the genetic etiology of patients with the clinical syndrome, presenting great potential for use in properly diagnosing in the genetic cause of the clinical syndrome.