Objective: To investigate whether The small nuclear RNA activating complex polypeptide 3 (SNAPC3) gene rs12093 polymorphism is associated with ischemic stroke (IS) and Traditional Chinese Medicine (TCM) syndromes of IS. Methods: This study enrolled 774 patients with ischemic stroke (IS) and 793 normal controls. Massarray technology was used for genotyping. And genetic association analysis was estimated by PLINK program. Results: ①SNAPC3 gene rs12093 polymorphism was significantly associated with the risk of ischemic stroke wind syndrome of IS [OR=0.76, 95%CI(0.58-0.99), P=0.047 in dominant model)]. ②After adjusting age and gender, SNAPC3 gene rs12093 polymorphism and the score of ischemic stroke wind syndrome(Padj=0.037 in additive model;Padj=0.009 in recessive model), the correlation is statistically significant. ③After adjusting age and gender, platelet (PLT) (Padj=0.024 in addiction model; Padj=0.039 in dominant model)and thrombin time(TT)(Padj=0.042 in dominant model) were significantly associated with rs12093 polymorphism in patients with ischemic stroke wind syndrome. Conclusion: SNAPC3 gene rs12093 polymorphism may affect the occurrence of ischemic stroke wind syndrome.