Objective To assess the long-term efficacy of enhanced ablation in pulmonary vein antrum (PVA) guided by remote magnetic navigation (RMN) in the patients with atrial fibrillation (AF). Methods From January 2013 to June 2015, 49 consecutive patients with refractory non-valvular AF who undergoing radiofrequency catheter ablation and voluntarily taking part in this study in our hospital were recruited in this study. They were randomized into a conventional ablation group (CAG, n=24) and an enhanced ablation group (EAG, n=25). PVA isolation was achieved by creating a single ablation circle in the patients of CAG group, and was double ablation circles at PVA in those of EAG group. An irrigated magnetic ablation catheter, CARTO 3 mapping system and Niobe magnetic navigation were used in both groups. A Lasso mapping catheter was used to confirm PVA isolation. Regular Holter monitoring was used to follow up all patients. Results PVA isolation succeeded in all the patients. Ablation energy delivery time was obviously longer in EAG group than in CAG group ［(45.66±6.59) vs (40.10±3.48) min, P<0.01］. There were no significant differences in fluoroscopic time, procedure time and venous NT-proBNP level between the 2 groups (P>0.05). During the follow-up of (19.3±5.6) months, Holter monitoring showed that the AF recurrence rate was remarkably lower in EAG group than in CAG group (8.00% vs 33.33%, P<0.05). Reconnection between left atrium and PV was confirmed in 8 relapsed patients during re-ablation, and reoperation was successful in all of them. Conclusion Enhanced PVA ablation effectively improves the long-term outcomes of AF and reduces the recurrence rate.