The effect of relaxation time in hyperbolic heat transfer model on the temperature field of microwave ablation of atrial fibrillation was investigated. And the results were compared with those calculated by Pennes model. A three-dimensional model of microwave ablation of atrial fibrillation was constructed. The relaxation time (τ) was 0, 1, 5, 8, 10, 15 and 20 s, respectively. And the temperature field of myocardial tissue was obtained. The results showed that the highest temperature of the hyperbolic model was 21.8 ℃ lower than that of the Pennes model at the beginning of ablation. With the increase of ablation time, the highest temperature tended to be the same. The lesion dimensions appeared at 3, 4, 6, 7, 8, 9, and 10 s, respectively after ablation. Therefore, the influence of hyperbolic model on temperature will decrease with the increase of the ablation time. At the beginning of ablation, the relaxation time will hinder the speed of myocardial thermal diffusion. The larger the relaxation time is, the slower the speed of thermal diffusion is. This study provides a reference for the application of hyperbolic model in microwave ablation of atrial fibrillation.