To investigate the clinical significance of the CHA2DS2-VASc-60 score, lipoprotein (a) [Lp(a)], red blood cell distribution width (RDW), and their combined effect in patients with non-valvular atrial fibrillation (NVAF) who experience acute ischemic stroke (AIS). This retrospective analysis was conducted on the clinical data of hospitalized patients with NVAF at the Third Affiliated Hospital of Anhui Medical University between April 1, 2020, and April 1, 2023. Based on the diagnosis of acute ischemic stroke (AIS), the patients were divided into two groups: the AIS group (150 cases of NVAF patients with comorbid AIS) and the non-AIS group (163 cases of NVAF patients without AIS). We performed CHA2DS2-VASc-60 scoring for all patients and collected their laboratory indicators and echocardiographic indicators during hospitalization. The study comprised 313 individuals with NVAF in total. There is a statistically significant difference (P < 0.05) in the comparison of CHA2DS2-VASc-60 score (5.68 ± 1.12 vs. 3.67 ± 1.47), Lp(a) [23.98 (13.28, 42.22) vs. 14.32 (7.96, 21.91)] and RDW (13.67 ± 1.25 vs. 12.94 ± 0.76) between NVAF patients with and without concomitant AIS. The results of the Spearman correlation analysis demonstrate a positive association between Lp(a) and RDW levels and both the CHA2DS2-VASc score and the CHA2DS2-VASc-60 score in patients with NVAF. Multivariate logistic regression analysis revealed that CHA2DS2-VASc-60 score [OR = 6.549, 95% CI: 4.110–10.433, P < 0.05], Lp(a) [OR = 1.023, 95% CI: 1.005–1.041, P < 0.05], and RDW [OR = 1.644, 95% CI: 1.071–2.525, P < 0.05] were independent risk factors for AIS in patients with non-valvular atrial fibrillation (NVAF). The receiver operator characteristic (ROC) curves showed that the area under the curve of CHA2DS2-VASc-60 score, Lp(a), RDW, and CHA2DS2-VASc-60 score combined with Lp(a) and RDW predicted that NVAF patients with AIS were 0.881 [95% CI: 0.804–0.906], 0.685 [95% CI: 0.626–0.744], 0.695 [95% CI: 0.637–0.754], and 0.906 [95% CI: 0.845–0.921], respectively. The CHA2DS2-VASc-60 score, Lp(a), and RDW were significantly increased in NVAF patients with AIS, which were independent risk factors for NVAF patients with AIS. The combination of the three has a high predictive capacity for NVAF patients with AIS.