Objective. To assess the predictive worth of HPV E6/E7 mRNA detection in the outcome of the cervical low-grade squamous intraepithelial lesion (LSIL). From September 2017 to early September 2019, patients screened for high-risk HPV positive or abnormal cervical liquid-based cytology were retrospectively analyzed and diagnosed with LSIL by cervical biopsy were recruited. The independent influencing factors of the regression of LSIL lesions after follow-up were analyzed, and the outcome of LSIL was calculated. The results of the initial colposcopy in this study were CIN I, CIN II/P16-negative, CIN II/P16-positive, and CIN III. At the time of re-examination, LSIL patients had three outcomes: regression, persistence, and progression. In the two follow-ups, 330 patients were finally included, including 276 CIN I patients (group A) and 54 CIN II/P16-negative patients (group B). The positive rates of HPV E6/E7 mRNA in each group were 66.67% and 70.37% for A and B, respectively. The total positive rate of E6/E7 mRNA was 67.27%, and there was no significant difference between the two groups (
P
>
0.05
). After 1 year follow-up, whether HPV E6/E7 mRNA regressed or was negative was associated with the outcome of LSIL-related lesions (
P
<
0.05
). The regression or negative rate of HPV E6/E7 mRNA was 1.57 times higher than the progression rate of HPV E6/E7 mRNA-positive diagnosis of LSIL lesions. Univariate logistic regression analysis showed that age at first sexual intercourse, HPV E6/E7 mRNA results, and lesion type were statistically significant (
P
<
0.05
). Whether HPV E6/E7 mRNA was negative (OR = 2.420,
P
=
0.001
) and age at first sexual intercourse ≥20 years (OR = 0.420,
P
=
0.002
) were independent influencing factors associated with LSIL regression. Multivariate logistic analysis showed that age of first sexual intercourse ≥20 years (OR = 0.420,
P
=
0.002
) and HPV E6/E7 mRNA-negative (OR = 2.420,
P
=
0.001
) were independent factors associated with LSIL. HPV E6/E7 mRNA detection can be used for predicting the outcome of LSIL and has a good application value.