Laser and radiofrequency ablation are two thermal ablation methods currently widely used to treat lower limb venous insufficiency. However, very few studies have been conducted on the use of microwaves, a form of thermal ablation, for the treatment of small saphenous vein (SSV) insufficiency. This study aimed to examine the efficacy and safety of endovenous microwave ablation (EMA) for the treatment of SSV insufficiency. The clinical data of 126 patients (126 lower limbs) with SSV insufficiency (SSV trunk reflux time ≥ 500ms on lower limb color Doppler ultrasound) treated at the Surgery Department of The Sixth People's Hospital of Zhuji from January 2020 to June 2022 were analyzed retrospectively; 64 patients underwent EMA and 62 underwent endovenous laser ablation (EVLA). The perioperative marker data [duration of surgery, duration of hospitalization, length of thermal ablation, duration of thermal ablation, number of incisions, and numerical pain rating scale (NPRS)], complication data [skin ecchymosis, skin burns, surgical site infection, paresthesia, deep vein thrombosis (DVT), and heat-induced thrombosis (EHIT)], venous clinical severity score (VCSS), chronic venous disease quality of life questionnaire (CIVIQ-20) before and 1, 3, 12months after surgery, and SSV trunk occlusion rate at 12months after surgery were compared between the two groups. No significant differences in the surgery or hospitalization durations were observed between the two groups. There were no significant differences in the length of the SSV that required thermal ablation between the two groups; however, the thermal ablation time was shorter in the EMA group than that in the EVLA group (6.14 ± 1.47min vs 7.05 ± 1.16min, P < 0.001). There were no statistical differences in the number of incisions, volume of tumescent solution used, or quantity of sclerosing foam used. The NPRS scores of the EMA group at 24h and 72h after surgery were significantly greater than those of the EVLA group (4.03 ± 0.98 vs 3.52 ± 1.28, P = 0.013; 3.78 ± 1.06 vs 3.15 ± 1.03, P = 0.001). Moreover, the two groups showed no significant difference in the NPRS score at 1month (1.14 ± 0.84 vs 1.07 ± 0.75, P = 0.623). The EMA and EVLA group patients experienced similar postoperative complications. The VCSS and CIVIQ-20 score significantly improved at 1, 3, and 12months after surgery. The VCSS and CIVIQ-20 scores were compared between the two groups at 12months after surgery, and there were no significant differences (1.44 ± 0.63 vs 1.56 ± 0.56, P = 0.261; 24.24 ± 4.96 vs 25.19 ± 5.36, P = 0.304). There was no significant difference in the incidence of SSV trunk occlusion at 12months after surgery between the two groups (95.31% vs 96.77%, OR 1.475; 95%CI 0.238-9.146, P = 1.000). EMA and EVLA are equally effective treatment methods for SSV insufficiency. EMA is associated with higher NPRS scores in the early postoperative period.