Objective To investigate the inhibitory effect of bone marrow mesenchymal stem cells (BMMSC) on the inflammatory response of microglial cells. Methods The samples were divided into four groups. Group Ⅰ: microglial (BV-2) cells were cultured in DMEM (high glucose). Group Ⅱ: BV-2 cells were cultured in DMEM containing lipopolysaccharide (LPS). Group Ⅲ: BV-2cells and BMMSCs were co-cultured in DMEM. Group Ⅳ: BMMSCs were cultured in DMEM containing LPS. The growth state and ultrastructure of BV-2 cells were observed and the changes of TNF-α expression were detected. Results Different cell densities of BV-2 cells were observed under the optical microscope in an order from high level to low level: group Ⅰ > group Ⅲ > group Ⅱ. The expressions of TNF-α were: group Ⅱ > group Ⅲ > group Ⅰ. Ultrastructural observation of BV-2 cells showed that there were a large number of swollen mitochondria and endoplasmic reticulum, some of them showed vacuolization. No BV-2 cells with multiple hucleoli were found in the group Ⅱ indicating the absence of active cell growth. At the same time, cytolysis was observed only in the group Ⅱ. The growth of BV-2 cells in the group Ⅲ was better than that in the group Ⅱ.Conclusions BMMSCs can inhibit inflammatory response of microglial cells, therefore, play a neuroprotective role.