In this paper, the gene mutation detection in the research group and the control group collected through the investigation and combined with clinical analysis, the following conclusions are drawn: several popular genes PAX9, MSX1, EDA, AXIN2, etc. Missing teeth and related diseases (cleft lip and palate, ectodermal hypoplasia, colorectal tumorigenesis, etc.)have research significance. Here, EDA is linked to cleft lip.