Objective: To analyze the cost-effectiveness of administering two doses of different types of human papillomavirus (HPV) vaccines to 12-year-old female adolescents. Methods: A decision tree Markov model with genital warts and cervical cancer as target diseases was established to analyze the effects, costs, and Quality Adjusted Life Years (QALY) of strategies such as no vaccination, two doses of bivalent HPV (HPV-2), two doses of quadrivalent HPV (HPV-4), and two doses of nine-valent HPV (HPV-9) in a 12-year-old female adolescent cohort in 2023 using 50% of the procurement price or self-funded vaccination price in pilot provinces. The number of avoided cases of cervical cancer and genital warts and the incremental cost-utility ratio (ICUR) were compared between different strategies. Results: Compared with non-vaccination, female adolescents who received two doses of HPV-2, HPV-4 and HPV-9 were able to avoid 55.2% of cervical cancer cases with HPV-2, 77.11% and 78.68% of genital warts with HPV-4, and 54.99% and 73.46% of cervical cancer with HPV-9, respectively. The ICUR of strategies HPV-2, HPV-4, and HPV-9 was -28 470.44 yuan/QALY, 29 328.26 yuan/QALY and 48 106.85 yuan/QALY, respectively. HPV-2 was the most economical strategy and could achieve net cost savings. Single-factor sensitivity analysis showed that the results were robust, and the most influential factors were discount rate, vaccine prices and direct medical costs for low-grade precancerous lesions. The probability sensitivity analysis showed that compared with the national gross domestic product (GDP) per capita in 2023, the probability of cost-utility of HPV-2, HPV-4 and HPV-9 compared with non-vaccination was 99.51%, 89.03% and 67.81%, respectively. Only when the price of a single dose of HPV-4 and HPV-9 vaccines was lower than 26.12% and 20.68% of the current self-funded vaccination price, respectively, could there be a net cost saving. Conclusion: In the case where HPV-2 adopts the pilot province procurement price and the multivalent vaccine adopts a 50% self-funded vaccination price, the vaccination of 12-year-old female adolescents with HPV-2, HPV-4 and HPV-9 has cost-effectiveness, and HPV-2 is the most economical strategy.