X-linked hypophosphatemic rickets (XLH) is caused by inactivating mutations in the PHEX gene and is the most common form of hereditary rickets. The treatment is more complicated compared with the general rickets. A family were admitted to the Department of Endocrinology, Hainan General Hospital in 2018. The proband was a 3-year-6-month-old female, Han nationality. She was admitted to hospitalization for bilateral knee valgus and walking instability. The patient's parents were not in consanguineous marrige, and there was no similar medical history in the family. The patient presented with "O" leg, bracelet sign, chicken breast, and low blood phosphorus. Typical change of rickets also appeared in her X-ray examination. The DNAs of the peripheral blood were extracted from the patient and her parents. All coding exons and flanking regions of PHEX gene in the patient were amplified by PCR, and the mutant sites of the family members were testified by a generation sequencing. A heterozygous variation (c.1482+5G>C) affecting splicing outcome was detected at the splicing region of intron 13 of PHEX gene in the patient. The variation has been included in the human gene mutation database (HGMD). No variation was found in the proband's parents, the PHEX gene in the patient was a de novo variation. Our research provided reference for the future genetic counseling for this patient and enriched the research data on the relationship between genotype and clinical manifestations.