INTRODUCTION Smoking has been proven to increase the risk of cervical cancer, but it is still controversial whether smoking reduces women’s ability to clear human papillomavirus (HPV) infection. This study investigated the association between smoking behaviors during follow-up and clearance of HPV infection in women with HPV-positive and pathologically normal uterine cervix in China, using a propensity score matching (PSM) analysis. METHODS The present prospective study included data from women examined in the Gynecology Department of Shanghai General Hospital from January 2018 to June 2020. Twenty patients who smoked throughout follow-up were selected and matched with 60 patients using the 1:3 PSM method on age, marital status, and whether infected with high-risk HPV (HR-HPV). At each visit, smoking and sexual behaviors were collected. The Kaplan–Meier method and a Cox proportional hazard regression model were used to evaluate the probability of clearing HPV infection within a 2-year follow-up. RESULTS A total of 80 patients were included in the study, all of whom were infected with at least one HR-HPV type at baseline. Current smokers had a lower likelihood of clearing the HPV infection than current non-smokers, after adjusting for a history of sexually transmitted diseases (STD), HPV infection status, and sexual behaviors during follow-up (AHR=0.478; 95% CI: 0.239–0.958, p=0.037). Additionally, longer duration, higher frequency and larger doses of smoking correlated with the lower clearance possibility of HPV infection (p for trend=0.029, 0.022 and 0.026, respectively). CONCLUSIONS This study showed that the use of tobacco throughout follow-up could increase the risk of a persistent HPV infection, this risk being higher for smokers with heavier tobacco consumption. Our results should alert HPV-positive women to reiterate the advice to cut-back on or stop smoking.