Spondyloepiphyseal dysplasia congenita was an extremely rare genetic disorder, which was mainly caused by pathogenic variants in COL2A1. We identified two novel heterozygous variants of c.1654G>A (p.Gly552Arg) in exon 25 and c.3518G>T (p.Gly1173Val) in exon 50 of COL2A1 in two unrelated Chinese families, which led to severe SEDC. Here, COL2A1 is linked to spondyloepiphyseal dysplasia congenita.