The anatomical and functional characteristics of the left atrial appendage (LAA) and its relationships with anatomical remodeling and ischemic stroke in patients with atrial fibrillation (AF) have not been clearly established. The purpose of this study was to determine whether functional and morphological features of the LAA independently predict clinical outcome and stroke in patients with AF who underwent catheter ablation (CA). Two hundred sixty-four patients with AF, including 176 with paroxysmal AF (PAF, 54.0 ± 11.4 years old, M:F = 138:38) and 88 with persistent AF (PeAF, 56.4 ± 9.6 years old, M:F = 74:14) were studied. Of these patients, 31 (11.7 %) had a history of stroke/TIA (transient ischemic attack). The LA and LAA volumes were 124.0 ± 42.4 and 24.9 ± 4.3 ml in PeAF, these values were greater than those in PAF (81.2 ± 24.8 ml and 21.2 ± 5.1 ml, P < 0.001). The AF type (P = 0.016) and AF duration (P = 0.005), and anti-arrhythmic drugs use (P < 0.001) were significant predictors of AF recurrence after CA in all patients. Compared with patients without history of stroke, stroke patients had larger LA volume (106.9 ± 23.0 vs. 94.0 ± 38.9 ml, P = 0.004) and had lower LAA EF (50.0 ± 11.0 vs. 65.7 ± 13.4 %, P < 0.001). The independent predictors of stroke were age (P = 0.002) and LAA EF (P < 0.001) in PAF patients and that was only age (P = 0.001) in PeAF patients. In anatomical and morphological parameters of the LA and LAA, only depressed systolic function of the LAA was significantly related to stroke/TIA and recurrence of AF after CA in paroxysmal AF patients. Further large scaled prospective study is required for validation.