Preimplantation genetic testing (PGT) is a precise and effective technique for detecting inherited pathogenic mutations to prevent birth defects. However, there are few reports on PGT for pseudo-autosomal genetic diseases. In this study, both X-linked and Y-linked short stature homeobox-containing (SHOX) gene mutations were identified in the Leri-Weill dyschondrosteosis (LWD) affected family, suggesting a de novo event of X–Y pseudo-autosomal homologous recombination during sperm meiosis in the common ancestor of the affected family members. A novel PGT strategy with sequential analysis of polar bodies and embryos (PGT-Sean) was applied to the SHOX mutation carriers. Following PGT-Sean, a healthy offspring was born to the LWD-affected family. For families with pseudo-autosomal genetic diseases and other genetic disorders linked to subtelomeric regions, in case of high recombination rates and lack of multiple region-specific markers, it is recommended to perform PGT-Sean to enable a more accurate clinical genetic diagnosis.