Objective: This study aimed to investigate the effectiveness of microwave therapy in clearing HPV infection. Methods: A retrospective study was performed on 181 HPV subclinical infection patients who were admitted to the Third Affiliated Hospital of Sun Yat-sen University from April 2011 to July 2015. The patients were divided into a microwave therapy group and a control group according to the therapeutic method they had received. Age, gravidity (G), parity (P), squamocolumnar junction (SCJ) types, HPV types, and HPV clearance and removal time were analyzed. The outcome of microwave therapy, the natural laws of HPV infection spontaneous clearance, and the influencing factors of HPV clearance were studied. Results: Ultimately, 165 patients were included in the study, with 47 cases in the microwave therapy group and 118 cases in the control group. There were no statistically significant differences in the baseline characteristics, including age, gravidity times, parity times, HPV types, and SCJ. The HPV clearance rate of microwave group was significantly higher than the rate of the control group. The median HPV clearance time of the microwave group was significantly shorter than the clearance time of the control group. There were no significant differences in age for the HPV clearance rate and clearance time. No significant differences were found in the high risk HPV and low-risk HPV patients for the HPV clearance rate and clearance time and no significant differences were found in the clearance rate and clearance time between the most common types of HPV. Conclusion: Microwave therapy is a safe and reliable treatment for cervical HPV subclinical infection, which can not only increase the clearance rate but also reduce the clearance time.