Objective: Gene set enrichment analysis (GSEA) and immune infiltration analysis were performed on chip data on carotid atherosclerosis expression profile. In order to explore the pathogenesis of carotid atherosclerosis. Method: The GSE43292 data were obtained from the gene expression omnibus (GEO). CIBERSORT deconvolution method was utilized to analyze the infiltration ratio of immune cells. Result: The up-regulated immune related biological processes include the regulation of cytokine stimulation response and B cell activation and immune response. The up-regulated immune related KEGG signaling pathway has natural killer cell mediated cytotoxicity, Fc epsilon RI signaling pathway, RIG-I like receptor signaling pathway and JAK-STAT signaling pathway. The down regulated immune related KEGG signaling pathway is transforming growth factor β signaling pathway. The results of immune infiltration analysis showed that Macrophages M0 and B cells memory were significantly increased in the vascular tissues of carotid atherosclerosis. B cells naive, T cells CD8, T cells regulatory, NK cells activated, Monocytes and Dendritic cells resting were significantly decreased. Conclusion: Adaptive immunity of B2 cells and NK cell cytotoxicity plays an important role in carotid atherosclerosis. Three pathways of KEGG may be significant factors in the pathogenesis of carotid atherosclerosis.