Purpose: To perform a meta-analysis of clinical trials comparing percutaneous microwave ablation (PMWA) guided by ultrasound with conventional thyroidectomy for the management of papillary thyroid microcarcinoma (PTMC), analyzing feasibility, safety, and long-term efficacy, and to provide clinical guidance for the treatment selection of PTMC. Methods: Embase, PubMed, Cochrane Library, Web of Science, CNKI, VIP Database, and Wanfang Database were systematically searched to identify clinical studies of PMWA or thyroidectomy for PTMC up to December 2023. The relevant data from the articles were extracted, and the data analysis was performed using RevMan 5.4 software. Results: A total of 442 articles were identified and subsequently screened based on the inclusion and exclusion criteria, 9 clinical studies involving a total of 1577 patients were included, with 788 patients in the PMWA group and 789 patients in the surgery group. Following data extraction and statistical analysis, in comparison to the surgery group, the PMWA group had shorter operation time [mean differences (MD) = -36.36; 95% CI -55.66 to -17.06; P = .0002], shorter hospital stay (MD = -3.93; 95% CI -5.55 to -2.30; P < .00001), less intraoperative bleeding (MD = -21.25; 95% CI -27.36 to -15.15; P < .00001), and lower hospital costs (MD = -1.00; 95% CI -1.33 to -0.66; P < .00001), all with statistical significance. The comparison of postoperative complications revealed a lower incidence of complications in the PMWA group compared to the surgery group [relative risk (RR) = 0.29; 95% CI 0.21 to 0.40; P < .00001], with statistical significance. Thyroid-related hormone analysis showed that the free triiodothyronine (MD = 0.61; 95% CI 0.33 to 0.90; P < .00001) and free thyroxine (MD = 1.81; 95% CI 0.94 to 2.68; P < .0001) levels in the PMWA group were higher than those in the traditional surgery group, while the levels of thyroid-stimulating hormone were lower than those in the traditional surgery group (MD = -7.63; 95% CI -10.25 to -5.01; P < .00001), with statistically significant differences, indicating that PMWA had a smaller impact on thyroid function. In 2 studies, there were no statistically significant disparities in postoperative recurrence or lymph node metastasis (LNM) between the 2 cohorts (RR = 0.70; 95% CI 0.33 to 1.50; P = .36). There were no statistically significant differences in physiological health score between different groups and different time points before and after treatment (P > .05); However, the mental component score and the total score of the Medical Outcomes Study (MOS) item short-form health survey were significantly elevated in the ablation group compared to the excision group post-treatment (P < .05). Conclusion: For patients with low-risk PTMC with definitive diagnosis and precise risk stratification, PMWA can be selected. PMWA treatment for patients with PTMC is comparable to conventional surgical treatment and has the advantages of minimal trauma, rapid recovery, no scarring, and fewer complications, which are superior to open surgery to a certain extent. For patients with ambiguous preoperative diagnosis and uncertainty regarding LNM status, surgical intervention is the optimal choice.