Congenital craniomaxillofacial deformities are common human growth and development defects. A long non-coding RNA (lncRNA) is an RNA longer than 200 nucleotides that are not predicted to be translated to a functional protein product. Recently, an increasing number of studies have shown that lncRNA have a critical role in processes of craniomaxillofacial development. In this paper, the research progress of long non-coding RNAs in craniomaxillofacial development and deformities was reviewed.