Objective To investigate the effect of non-pulmonary vein trigger ablation combined with pulmonary vein isolation on the long-term prognosis of paroxysmal atrial fibrillation patients with low ejection fraction. Methods A total of 87 patients with paroxysmal atrial fibrillation and left ventricular ejection fraction (LVEF) <45% who were treated by catheter ablation in Tianjin 5th Central Hospital were enrolled. The patients were divided into group I (non-pulmonary vein trigger ablation combined with pulmonary vein isolation) and group Ⅱ (pulmonary vein isolation) according to the treatment modalities. After 2 years of follow-up, Log-rank χ2 was used to compare the prognosis of the two groups, and the factors affecting postoperative recurrence in the patients was analyzed by Cox regression. Results At the end of follow-up, the 2-year success rate of operation and LVEF in the group I were higher than those in the group Ⅱ (P < 0.05), while the number of recurrence patients with non-pulmonary vein trigger in the group Ⅱ was larger than that in the group I (P < 0.05). Coronary artery disease, non-pulmonary vein triggering lesions, non-pulmonary venous trigger ablation and LVEF were the independent influencing factors for postoperative recurrence in atrial fibrillation patients with low ejection fraction (P < 0.05). Conclusions Pulmonary vein isolation combined with non-pulmonary vein trigger ablation has good long-term effect on atrial fibrillation patients with low ejection fraction.