The study attempted to clarify the protective role of bone marrow-derived mesenchymal stem cell (BMSC) transplantation on LPS-induced acute lung injury (ALI) of rats. BMSC were obtained from bone marrow of rat, cultured and proliferated in vitro. Rats of ALI were established through lipopolysaccharide (LPS) administration. Male rats were allocated to control group, ALI group and BMSC, transplantation group. Rats were sacrificed after BMSC injection after 12h, 24h and 48h. Here we investigated the role of BMSC in LPS-induced alveolar macrophages to further demonstrate the mechanism of BMSC to lung injury. TLR3, a member of Toll-like receptor family, has been found in macrophages and the cell surface. In our study, first BMSC successfully reversed LPS-induced lung injury by hematoxylin-eosin (H&E) staining, ameliorated apoptosis via TUNEL and flow cytometer analysis, as well as improved cell structure. And then, western blot, quantitative real-time PCR, immunohistochemistry and immunofluorescence analysis were used to confirm that TLR3 was significantly down-regulated for BMSC treatment. Subsequently, TRIF and RIP1, down-streaming signals of TLR3, were inhibited greatly, leading to TRAF3, MAPK as well as NF-κB inactivity. Our results indicated that BMSC transplantation group displayed inhibitory effects on interferon (IFNs) levels via TLR3 in LPS-induced ALI and preventive effects on inflammation response via TLR3-regualted MAPK and NF-κB signaling pathway in LPS-induced lung injury. The present study indicated that BMSC could display protective effects on LPS-induced ALI and provide an experimental basis for clinical therapy.