Congenital craniofacial dysmorphology is a common disease in oral and maxillofacial surgery that is mainly caused by gene mutation. This disease affects the morphology and function of craniofacial organs. It usually is accompanied by eustachian tube dysfunction and otitis media, which cause hearing impairment. The SH3PXD2b gene is a newly discovered podosome adaptor protein that significantly affects podosome formation, extracellular matrix remodeling, and craniofacial organ development. This article reviews the SH3PXD2b gene, SH3PXD2b gene mutation, and its relationship with craniofacial dysmorphology and otitis media.