Objective: To explore application value of high-risk human papillomavirus (HR-HPV) deoxyribonucleic acid (DNA) polymerase chain reaction (PCR) detection in the screening of cervical intraepithelial neoplasia (CIN). Methods: A total of 98 female patients undergoing CIN screening in the hospital were retrospectively enrolled as the research objects between June 2023 and September 2025. The cervical secretions were detected by HR-HPV DNA PCR and Thinprep cytologic test (TCT). Taking the results of histopathological examination as the golden standard, the sensitivity, specificity, accuracy, missed diagnosis rate, misdiagnosis rate, positive predictive value and negative predictive value of the two methods in CIN screening were compared. Results: The results of histopathological examination showed that there were 32 positive cases and 66 negative cases. The sensitivity and accuracy of HR-HPV DNA PCR for screening CIN were 95.24% and 86.73%, higher than those of TCT (50.00%, 75.51%, P<0.05). The negative predictive value of HR-HPV DNA PCR was higher than that of TCT (98.48% vs 81.08%, P<0.05). The missed diagnosis rate of HR-HPV DNA PCR was lower than that of TCT (4.76% vs 50.00%, P<0.05). Conclusion: Both TCT and HR-HPV DNA PCR have good screening value in CIN. HR-HPV DNA PCR has higher screening value and is worthy of further clinical research and application.