Sporadic thumb polydactyly with nonfamily inheritance is the most common in clinical work. This study focused on characterization of GLI3 gene function. We constructed the plasmid with p.m948i point mutation of GLI3 and transfected it into mouse embryonic fibroblasts (MEFs) to study the effects and potential mechanism of the mutant gene. The RNA of GLI3 mutant cells was extracted and analyzed by transcriptome sequencing and bioinformatics. Finally, we constructed cbx3 overexpression plasmid, designed siRNA for gene silencing, and transfected it into the MEFs. Cell proliferation and invasion ability of the MEFs were examined. The results showed that there were 2,452 differential expression genes in the MEFs transfected with GLI3 mutant plasmid compared with wild-type MEFs. The results of differential expression analysis showed that the cbx3 gene was significantly up-regulated. Overexpression of cbx3 in MEFs promoted cell proliferation and invasion, while siRNA knockdown of cbx3 expression reduced proliferation and invasion. GLI3 gene mutation in MEFs resulted in cbx3 up-regulation and promoted MEF proliferation and invasion. This study further clarified the potential function of GLI3 in limb development, established a new relationship between gene mutation and polydactyly, and preliminarily clarified the possible signal pathway, all of which have laid a foundation for further study on the etiology of polydactyl.