Objective To compare the postoperative hypocalcemia between ultrasound-guided microwave ablation (MWA) and total parathyroidectomy (TPTX) for secondary hyperparathyroidism (SHPT). Methods The retrospective study reviewed 286 SHPT patients (171 received MWA and 115 underwent TPTX) between March 2018 and May 2019. Propensity-score matching was used to assemble a cohort of patients with similar baseline characteristics. A total of 184 SHPT patients (92 in each group) were finally enrolled, the occurrence and prognosis of postoperative hypocalcemia were compared. And the risk factors associated with severe hypocalcemia (SH) in each group were analyzed. Results Hypocalcemia encountered in 95cases (49 in the MWA group and 46 in the TPTX group). SH occurred in 76 cases (40 in the MWA group and 36 in the TPTX group). There were no statistically significant differences in the detection time, incidence, minimum value of serum calcium and symptomatic hypocalcemia between MWA and TPTX group (allpvalues > 0.05). Of patients developing hypocalcemia, serum calcium did not recover to normal range in 5 cases (10.2%) in the MWA group, while 13 cases (28.3%) were still hypocalcemia at 6 months follow-up in TPTX group (p = 0.035). The time to recovery from hypocalcemia in the TPTX group (mean 30 days, range 3-180 days) was longer than the WA group (mean 14 days, range 3-126 days) (p = 0.000). High serum alkaline phosphatase (ALP) level and low serum calcium level were the main risk factors of postoperative SH. Conclusion There was no difference in hypocalcemia between MWA and TPTX group. Hypocalcemia in the TPTX group might need a longer time to recover.