Objective: To analyze the effect of Quyu Tongluo Decoction on acute cerebral infarction (ACI) patients and its influence on markers of brain injury. Methods: 83 patients with ACI admitted to our hospital from March 2021 to September 2023 were selected as the study objects. Patients were divided into control group (n=41) and study group (n=42) according to random number table method. The control group received conventional Western medicine treatment; Study group combined Quyu Tongluo decoction treatment. The therapeutic effects, brain injury markers (S100β), neuron-specific enolase (NSE) levels and adverse reactions of the two groups were analyzed and compared. Results: The total effective rate of the study group was significantly higher than that of the control group (P < 0.05). After treatment, the levels of S100β and NSE in both groups were decreased, and the reduction in the study group was significantly greater than that in the control group (P < 0.05). There was no significant difference in the incidence of adverse reactions between the two groups (P > 0.05). Conclusion: Quyu Tongluo Decoction can improve the therapeutic effect of ACI, play the role of brain protection, and do not increase the adverse reaction.