Spondylometaphyseal dysplasia (SMD) is an extremely rare disorder of irregular development of spine and metaphyses of long tubular bones. Mutations in the collagen type X alpha 1 gene were found to underlie this condition. Previously reported mutations in the N-terminal non-collagenous NC2 domain and C-terminal non-collagenous NC1 domain failed to be identified in some specific patients. A 23-year-old male was referred to us for fixed, angular thoracolumbar kyphosis with semi-paralysis, numbness, and tremor on his left lower limb. Marked hypoplasia of thoracolumbar vertebra and spinal canal stenosis were observed on radiology. He was diagnosed with spondylometaphyseal dysplasia (Type A4). Gene sequencing was performed using normalized targeted regions sequencing (TRS). A novel heterozygous missense variant p.Gly139Cys in the triple-helical region. Multiple lines of evidence imply this mutation to be pathogenic. Posterior instrumentation and vertebral column resection were given to correct his fixed, angular thoracolumbar kyphosis. The correction was satisfying and the functional outcomes were good. The findings corroborated that type X collagen plays a critical role in the formation of the human spine as well as the long bones, and further expanded the range of type X collagenopathy. Surgical procedure could be considered for patients with severe malformation and neurological impairments.