Horny Goat Weed is a commonly used in Chinese herbal medicine. And it is used in multiple kinds of diseases including cardiovascular diseases. Icariin is the major component isolated from Horny Goat Weed. It is reported to have lipid-lowering effect. In atherosclerosis, icariin attenuate the enhanced prothrombotic state independently of its lipid-lowering effects. However, its detail mechanism is remaining unclear. This study aimed to investigate the effect and mechanism of icariin on atherosclerosis. We performed gene expression profiling on icariin treated LPS-stimulated RAW264.7 and its control cells. Microarray analyses identified a list of genes significantly differentially expressed after icariin treated including downregulation of CX3CR1. Apoe null mice were assigned into 3 groups: control group, diet with 30 mg/kg/d icariin and diet with 60 mg/kg/d icariin. The results showed that icariin treatment significantly reduced lesion area and macrophage infiltration. Also icariin reduced CX3CR1 and CX3CL1 protein levels in the artery wall. In conclusion, icariin could be a potential anti-atherosclerosis agent by downregulating the expression of CX3CR1.