Objective To investigate the clinical effect of Naoxintong Capsule combined with warfarin in the treatment of non-valvular atrial fibrillation with acute cerebral infarction. Methods A total of 76 patients with non-valvular atrial fibrillation and acute cerebral infarction who were admitted to our hospital from May 2018 to May 2019 were enrolled as subjects, and according to the odd or even number of medical records, the patients were divided into treatment group A (treated with warfarin) and treatment group B (treated with Naoxintong Capsule combined with warfarin), with 38 patients in each group. Treatment outcome was compared between the two groups. Results Treatment group B had a significantly higher overall response rate than treatment group A (P<0.05). Compared with treatment group A after treatment, treatment group B had significantly lower NIHSS score and fibrinogen (P<0.05) and significantly longer thrombin time, prothrombin time, and activated partial thromboplastin time (P<0.05). Treatment group B had significantly lower incidence rate of adverse events and recurrence rate of cerebral infarction than treatment group A (P<0.05). Conclusion Naoxintong Capsule combined with warfarin has a good clinical effect in the treatment of patients with non-valvular atrial fibrillation and acute cerebral infarction and can effectively improve patient's neurological function and prevent the recurrence of cerebral infarction.