Objective: This study aimed to investigate the roles of high-risk human papilloma virus (HR-HPV) E6/E7mRNA in triaging patients negative for intraepithelial lesion (NILM) accompanied with HPV16/18 infection. Materials and Methods: A total of 514 female patients simultaneously underwent cytological assay, HPV-DNA assay, E6/E7mRNA detection, and colposcopic biopsy were selected. The study endpoint was the histologically confirmed high-grade cervical intraepithelial neoplasia (CIN) II or higher(II+). Results: The positive rates of E6/E7mRNA in histopathologically confirmed cervicitis, CIN I, CIN II, CIN III, and cervical cancer were 53.4%, 66.7%, 89.9%, 91.4%, and 100%, respectively. Among the patients that underwent the colposcopic biopsy due to cytological NILM plus HPV16/18 infection, the positive predictive values of HPV16/18 and E6/E7mRNA towards high-grade cervical lesions were 21.5% and 40.4%, respectively, and the comparison between these two factors showed statistically significant difference (p < 0.05). The negative predictive value of E6/E7mRNA was 97.8%. Conclusions: E6/E7mRNA showed good triaging effects towards the patients with cytological NILM plus HPV16/18 infection and could significantly reduce colposcopy and biopsy.