Objective: To investigate the distribution characteristics of HPV16 E6 gene 295T/G and E7 gene 647A/G variants in different cervical tissues in Xinjiang, to study the effects of these two loci on the expression of molecules in IFNκ and its pathway, to explore the molecular mechanism of their roles, and to analyse the relationship between these two variants and the occurrence and development of cervical cancer. Methods: (1) A total of 461 cervical paraffin-embedded tissue samples were collected and tissue DNA was extracted to detect the type of HPV infection by PCR, and the distribution of HPV16 viral E6-T295G and E7-A647G variants in cervical tissues was analysed by Sanger sequencing. Immunohistochemistry was used to detect the expression of IFNκ and molecules on its pathway including IFNκ, STAT1, IRF9, IFI27, IFI44L,OAS1 in cervical cancer and normal cervical tissues. Results: (1) The HPV16 infection rate of cervical paraffin-embedded tissue samples from women in Xinjiang region was 64.0% by PCR. And the HPV16 infection rate of Uyghur was 75.7%, of which the infection rate of Uyghur CIN1 and CIN2 with HPV16 was 60.6%, and the infection rate of CIN3 and cervical cancer was 82.9%. The HPV16 infection rate of Han ethnic group was 54.5%, among which the infection rate of Han ethnic group CIN1 and CIN2 of HPV16 was 34.0%, and the infection rate of CIN3 and cervical cancer was 66.5%. (2) The variant rate of Uyghur CIN1 patients presenting with E6-295T/G variant was 41.7%, and the variant rate of squamous cervical cancer patients presenting with E6-295T/G variant was 43.4%. The variant rate of Han ethnic group CIN1 patients presenting with the E6-295T/G variant was 33.3%, and the variant rate of squamous cervical cancer patients presenting with the E6-295T/G variant was 16.1%. The variant rate of Uyghur CIN1 patients presenting with the E7-647A/G variant was 41.7%, and the variant rate of squamous cervical cancer patients presenting with the E7-647A/G variant was 9.2%. The variant rate of E7-647A/G variant was 45.8% in Han ethnic group of CIN1 patients and 50.0% in squamous cervical cancer patients. (3) The results showed that the expression of IFNκ, IRF9, OAS1, IFI27, and IFI44L molecules on the IFNκ pathway was higher in normal cervical tissues uninfected with HPV than that of CIN1 with HPV infection, and the difference was statistically significant ( P<0.05). The expression of IFNκ, STAT1, IRF9, OAS1, IFI27, IFI44L molecules in CIN3, moderately differentiated, poorly differentiated cervical squamous carcinoma and adenocarcinoma were higher than that of CIN1, and the molecular expression of IFN-κ and its pathway in cervical squamous cell carcinoma and adenocarcinoma was higher than that in normal tissues, and the difference was statistically significant ( P<0.05). Conclusion: The rate of E6-295T/G variation in cervical cancer patients infected with HPV16 in Uyghur is higher than that in Han, while the rate of E7-647A/G variation in cervical cancer patients infected with HPV16 in Han is higher than that in Uyghur.