Background Microwave ablation (MWA) is an organ-preserving minimally invasive option for symptomatic benign thyroid nodules. Comparative evidence on thyroid function preservation after MWA versus surgical resection (SR) remains limited, particularly when postoperative hormone replacement is separated by surgical extent. Methods We retrospectively analyzed 113 consecutive adults treated with ultrasound-guided MWA or SR for symptomatic or cosmetically concerning cytologically benign thyroid nodules between January 2022 and October 2024. Patients with abnormal preoperative thyroid function, hyperfunctioning nodules, known autoimmune thyroiditis, prior thyroid surgery, indeterminate or malignant cytology, pregnancy, or concurrent thyroid malignancy were excluded. One-to-one propensity score matching was performed using eight pre-specified baseline covariates, yielding 48 matched pairs. The primary outcome was thyroid hormone dependence at 12 months, reported as overall dependence and, separately, as new-onset hypothyroidism after organ-preserving procedures. Secondary outcomes included operative duration, blood loss, hospital stay, 12-month symptom score, complications, recurrence, and volume reduction rate (VRR) after MWA. Results After matching, baseline characteristics were well balanced. MWA was associated with shorter operative duration (median 18.0 vs. 63.5 minutes), lower blood loss (1.5 vs. 53.5 mL), and shorter hospital stay (1.0 vs. 5.0 days; all P < 0.001). In the MWA group, median VRR reached 86.2% at 12 months. Symptom scores improved substantially from baseline in both groups (both P < 0.001), with comparable low 12-month symptom burden. Overall thyroid hormone dependence occurred in 1 of 48 MWA patients (2.1%) and 25 of 48 SR patients (52.1%). In the SR group, this included planned replacement after total thyroidectomy (14/14, 100%) and new-onset hypothyroidism after lobectomy or subtotal thyroidectomy (11/34, 32.4%). In the sensitivity analysis excluding total thyroidectomy, new-onset hypothyroidism remained lower after MWA (2.1% vs. 32.4%; P < 0.001). Conclusions In selected patients with small-to-moderate symptomatic benign thyroid nodules, MWA achieved substantial nodule shrinkage and low symptom burden at 12 months while reducing perioperative burden and postoperative hormone dependence. These findings support MWA as an organ-preserving alternative to surgery in appropriately selected patients, although randomized multicenter studies with longer follow-up are needed.