Variant pulmonary vein anatomy (PVA) has been reported to influence the recurrence of atrial fibrillation (AF) after radiofrequency ablation. However, the effects of PVA on AF in patients undergoing cryoballoon ablation (CBA) remain unknown. The present study aimed to examine the impact of PVA on the long-term outcome of CBA for AF. A total of 78 patients (mean age 60.7±10.9 years, 64.1% males) with symptomatic and drug-refractory paroxysmal AF were enrolled in the study. Left atrium (LA) and PVA acquired at computed tomography angiography (CTA) were reconstructed with CARTO® 3 SYSTEM. Patients were routinely evaluated by 24-hour Holter monitoring following CBA. Cox regression was used to detect the predictors of AF recurrence after CBA. The results showed abnormal PVA in 30 patients (38.5%) and 18 patients (23.1%) had left common PV (LCPV). Electrical pulmonary vein isolation was achieved in all patients. After a mean follow-up of 689.5±103.8 days, it was found that patients with abnormal PVA had similar AF recurrence rate to those with normal PVA (26.7% vs. 25.0%, P=0.54), and there was no significant difference in AF recurrence rate between LCPV patients and non-LCPV patients (33.7% vs. 23.3%, P=0.29). Cox regression analysis showed that AF duration (72.9±9.0 vs. 42.3±43.2 months, HR 1.001; 95%CI 1.003-1.014; P<0.001) and cryo-applications of right-side PVs (3.0±1.6 vs. 4.7±1.7, HR 0.661; 95% CI 0.473-0.925; P=0.016) were independent predictors of freedom from AF, but PVA was not identified as a predictor of long-term success. In conclusion, the variant PVA cannot significantly influence the long-term outcome of AF patients undergoing CBA; longer AF duration and less cryo-applications of right-side PVs are associated with higher AF recurrent rate.