Congenital cranial dysinnervation disorders(CCDDs)are a group of diseases with congenital non-progressive developmental abnormalities or absence of one or more cranial nerves, resulting in primary or secondary abnormalities of cranial nerves innervating the extraocular muscles. CCDDs can be sporadic or hereditary, and may be accompanied by systemic abnormalities. In recent years, with the research progress of neuropathology, neuroimaging, and genetics, it has not only been clarified that the cause of eye movement disorder in CCDDs is neurogenic, but also been found the pathogenic genes of CCDDs, including SALL4, HOXA1, KIF21A, PHOX2A, TUBB3, and HOXB1, etc. In this review, the relevant domestic and international literatures on the molecular genetics and neuroscience of CCDDs in recent years are reviewed, aiming to address how the causing gene mutations of CCDDs affect brain neural development and further lead to congenital abnormal cranial nerve innervation, in order to provide references for the clinical and basic research of CCDDs.