Treatment of recurrent brain metastases is extremely challenging. Here, we evaluated the feasibility and efficacy of an individualized three-dimensional template combined with MR-guided iodine-125 (125I) brachytherapy in the treatment of recurrent brain metastases. Twenty-eight patients with recurrent 38 brain metastases underwent 125I brachytherapy from December, 2017 to January, 2021. A pre-treatment brachytherapy plan and three-dimensional template were generated according to isovoxel T1-weighted MR images. 125I seeds were implanted under the guidance of three-dimensional template and 1.0-T open MR imaging. Dosimetry verification was performed based on CT/MR fusion images. Pre-operative and post-operative dosimetry parameters of D90, V100, and conformity index (CI) were compared. Overall response rate (ORR), disease control rate (DCR) at 6 months, and 1-year survival rate were calculated. Median overall survival (OS) measured from the date of 125I brachytherapy was estimated using Kaplan-Meier method. No significant differences were observed between pre-operative and post-operative D90, V100, and CI values (p > 0.05). The ORR and DCR at 6 months were 91.3% and 95.7%, respectively. The 1-year survival rate was 57.1%. The median OS was 14.1 months. Two cases of minor hemorrhage and 5 cases of symptomatic brain edema were observed during the study. All clinical symptoms were alleviated after corticosteroid treatment applied for 7 to 14 days. A three-dimensional template combined with MR-guided 125I brachytherapy in the treatment of recurrent brain metastases is feasible, safe, and effective. This novel 125I brachytherapy strategy is an attractive alternative in the treatment of brain metastases.