Background: To observe the medium-and long-term clinical efficacy and safety of radioactive 125I seed implantation for refractory malignant tumors based on a CT-guided 3D template-assisted technique. Methods: Twenty-five patients with refractory malignant tumors who received radioactive 125I seed implantation based on a CT-guided 3D template-assisted technique were selected. The post-operative adverse reactions were recorded; the number of puncture needles and particles used in the operation, dosimetric parameters, post-operative physical strength scores, and tumor response were statistically analyzed. The overall survival time and survival rate were counted, and the effect and prognosis were assessed. Results: 125I seed implantation was successful in all patients and no serious complications occurred. The average number of implanted puncture needles was 17 (19.12±13.00) and the median number of particles was 52 (55.12±32.97). The D90 in the post-operative clinical target volume (CTV) (93.24±15.70 Gy) was slightly lower than pre-operative CTV (93.92±17.60 Gy; P>0.05). The D90 in the postoperative planning target volume (PTV) (142.16±22.25 Gy) was lower than the pre-operative PTV (145.32±23.48 Gy; P>0.05). The tumor responses at 6 months post-operatively: complete remission (CR), 20%(5/25); partial remission (PR), 48%(12/25); stable disease (SD), 24%(6/25); progressive disease (PD), 8%(2/25); CR+PR, 68%(17/25); and local control rate, 92%(23/25). The 6-, 12-, and 24-month survival rates were 100%, 88%, and 52%, respectively. The post-operative physical strength score (Karnofsky performance score, KPS) exhibited a gradual trend towards recovery, which rose to the highest value 12 months after seed implantation, then decreased slightly, but the average score was still > 90 points. There was one intra-operative pneumothorax and two patients with superficial malignant tumors developed skin ulcerations. Multivariate analysis of prognosis showed that tumor sites and types were independent risk factors affecting survival. The number of needles and particles, and template type were not factors that affected prognosis. Conclusions: 3D template combined with CT-guided radioactive 125I seed implantation was shown to improve the rational distribution of radiation dose in the tumor target area because accurate radioactive 125I particle implantation was achieved. It has fewer complications and can further extend the overall survival and quality of life in patients with refractory malignant tumors.