Objective To investigate the clinical characteristics and diagnostics of Kozlowski type spondylometaphyseal dysplasia (SMDK). Methods The clinical features, laboratory tests and genetic testing of one SMDK case were analyzed. Results A eight-year-old male patient had more than 6 years course of disease. The clinical manifestations were stubby limbs, fingers and toes, varus deformity, knee valgus deformity, scoliosis and lordosis and severe metaphyseal changes. The heterozygous mutations were detected in TRPV4 and NXX3-2 genes. Conclusions Typical clinical features combined with genetic diagnosis facilitate early detection and accurate diagnosis of SMDK.