The relationship between atrial fibrillation (AF) type and stroke risk is still controversial. We investigated the difference of burden of atrial ectopic beats in different types of AF and the effect of the AF type on stroke risk in patients with non-valvular AF. In the prospective, multicenter observational registry with more than about 10,000 AF patients, 8883 non-valvular AF patients (mean age, 67.0 years; 36% were women) with eligible follow-up visits participated. We compared the burden of ectopic beats and stroke risk between patients with paroxysmal AF (n = 5,808) and non-paroxysmal AF (n = 3,075). The patients with a non-paroxysmal type of AF were older, male-predominant and had a higher prevalence of comorbidities and had more anticoagulation and rhythm control treatment than those with paroxysmal AF. In terms of the difference in burden of ectopic beats, patients with non-paroxysmal AF had a higher proportion of atrial premature beats (APBs) (paroxysmal vs. non-paroxysmal, median 3% vs. 5%; p = 0.001) in 24 hours Holter monitoring. During a median follow-up period of 16.8 months (Interquartile range [IQR], 11.67–20.52), a total of 82 (0.92%) patients experienced ischemic stroke with incidence rates of 0.50 and 1.09 events per 100 person-year for paroxysmal and non-paroxysmal AF, respectively. The cumulative incidence of stroke events was significantly higher in non-paroxysmal AF than in paroxysmal AF (p < 0.001). The risk of ischemic stroke was higher in non-paroxysmal AF with an adjusted hazard ratio (HR) of 2.08 (95% confidence interval [CI], 1.33–3.25; p = 0.001) than in paroxysmal AF. The type of AF was associated with an increased risk of stroke, along with the difference of burden of ectopic beats (specially in APBs) in different types of AF. These results suggest that the type of AF should be considered in stroke prevention and decision-making for oral anticoagulation in AF patients.