Background. This study aimed to explore the clinical study of clopidogrel combined with Huoxue Tongluo prescription in improving transient ischemic attack (TIA) and the effect on MMP-9, Hcy, and CRP. Methods. A total of 84 patients with TIA admitted to our hospital from December 2019 to February 2021 were selected. The patients were divided into the control group (42 cases: not treated with Huoxue Tongluo prescription) and study group (42 cases: treatment with Huoxue Tongluo prescription). The clinical efficacy, adverse reactions, the levels of blood pressure and lipid, blood rheology and cerebral hemodynamics, neurological function-related indicators, MMP-9, Hcy, and CRP of the two groups were compared. Results. The total effective rate in the study group was higher than the control group. Compared with before treatment, the levels of SBP and DBP in both groups decreased memorably after treatment, and those in the study group decreased more particularly than the control group. The levels of LDL, HDL, TC, and TG in the study group were significantly better than those in the control group. The plasma viscosity, whole blood high shear viscosity, whole blood low shear viscosity, and hematocrit of patients in the study group were lower than those in the control group, and the maximum blood flow velocity, minimum blood flow velocity, average blood flow velocity, and average blood flow were higher than those in the control group. The levels of NSE, MBP, and S100β in the study group were more memorably lower than those in the control group. After treatment, the levels of MMP-9, Hcy, and CRP in the study group were significantly lower than those in the control group. There was no obvious difference in the incidence of adverse reactions between the study group and control group. Conclusion. Clopidogrel combined with Huoxue Tongluo prescription can significantly improve the therapeutic effect and reduce the levels of MMP-9, Hcy, and CRP in patients with TIA.