Multiple epiphyseal dysplasia (MED) is a mild osteochondrodysplasia characterized by mild to moderate short stature and early-onset osteoarthritis. In this study, we found a family with MED with no linkage to known pathogenic genes. Whole-exome sequencing revealed a missense mutation (c.1076T>G, p.Leu359Arg， NM_001166412.2) in SPARC-related modular calcium binding 2 (SMOC2). We generated a mouse model by knocking-in the Smoc2 mutation. Mutant mice showed short-limbed dwarfism, disorganized and hypocellular proliferative zones and expanded hypertrophic zones in tibial growth plates. Study of the interaction between MED proteins and SMOC2 showed that SMOC2 and its extracellular calcium-binding (EC) domain could interact with collagen type IX α-1 (COL9A1), however, mutant SMOC2 could not. Our data indicated that SMOC2 mutation is responsible for the MED phenotype. The mutation in SMOC2 affected the interaction between SMOC2 and COL9A1.