Mesoporous silica is widely used because of its unique and excellent properties, especially it can be used as a drug carrier and gene carrier in the biomedical field. After the mesoporous silica is put into clinical use, it is more likely to be exposed in human body. Therefore, the effect of mesoporous silica on human body cannot be ignored. The injury of vascular endothelial cells is a prerequisite for the occurrence of many cardiovascular diseases. As a drug and gene carrier, mesoporous silica increases its contact with vascular endothelial cells, so its toxic effect on cardiovascular system cannot be ignored. In this study, amino (NH2 ) and carboxyl (COOH) were modified on mesoporous silica SBA-15 by post-grafting. The results showed that it still maintained the one-dimensional hexagonal mesoporous structure of SBA-15 and had typical mesoporous structure. Then human umbilical vein endothelial cells (HUVECs) were infected with SBA-15, NH2 -SBA-15, and COOH-SBA-15. The results showed that the functionalized mesoporous silica SBA-15 had cytotoxicity to HUVECs and damaged the cell membrane, but compared with the unmodified mesoporous silica SBA-15 the cytotoxicity of functionalized mesoporous silica SBA-15 was lower and the toxicity of carboxyl modified group was the lowest. By comparing the cell inhibition rate and the expression level of lactate dehydrogenate and reactive oxygen species induced by the three materials, oxidative damage and cell membrane damage may be two mechanisms of cytotoxicity. Mesoporous silica SBA-15 has an effect on cardiovascular system by inducing the high expression of nitric oxide, intercellular adhesive molecule-1 and vascular cell adhesive molecule-1 in HUVECs. In summary, our results show that mesoporous silica is toxic to vascular endothelial cells.