Background: Microwave ablation (MWA) can be used to treat severe secondary hyperparathyroidism; however, its efficacy and the predictor of its efficacy are unclear. In this retrospective study we determined the predictor of efficacy of MWA and compared the efficacy of MWA and parathyroidectomy. Materials and methods: Patients with severe secondary hyperparathyroidism who had received MWA or parathyroidectomy were enrolled in the study. Participants with MWA were divided into response and no response groups based on efficacy. Possible predictors were analysed using logistic regression to determine efficacy predictors. The participants were divided into MWA and parathyroidectomy groups, and the efficacy (including rates of achieving recommended goals for intact parathyroid hormone (iPTH), calcium, and phosphorus levels) were compared between the two groups. Results: Thirty-one participants were enrolled for predictor analysis. Only baseline iPTH level predicted efficacy (OR 0.997, P = 0.018). The optimal threshold value of iPTH for predicting efficacy was 1493.5 pg/mL. To compare efficacy, 30 patients were enrolled in MWA (18/30) and parathyroidectomy (12/30) groups. The rates of achieving recommended goals for iPTH levels varied between 0 and 60%; a significant difference was found between the groups at 5 months (P = 0.01). However, in the parathyroidectomy group, the iPTH level and rate of iPTH <124 pg/mL (lower limit of target range) were significantly lower than in the MWA group after treatment (40-75% versus 0-16.7%). Conclusion: Baseline iPTH level is a good predictor of MWA efficacy for severe secondary hyperparathyroidism; parathyroidectomy is more effective for severe secondary hyperparathyroidism than MWA.