Explored the appropriate way for bone marrow mesenchymal stem cells (bmMSCs) infuse in rat models of severe acute pancreatitis. Severe AP was induced in Sprage-Dawley rats by the sodium taurocholate bile duct retrograde injection. Rats were randomly divided into five groups: control group, SAP group, SAP +bmMSCs (tail vein) group, SAP + bmMSCs (intraperitoneal) group and SAP + bmMSCs (tail vein + intraperitoneal) group. In bmMSCs infused groups, bmMSCs labeled with DAPI were injected via the tail vein, intraperitoneal and via tail vein + intraperitoneal respectively 3 h after SAP. Rats were sacrificed on days 1, 2 and 3, and pancreatic tissues and the blood were collected. The levels of serum anti-inflammatory cytokines IL-10 and inflammatory cytokines (IL-1β, TNF-α, IL-6) were determined. Pathological changes of the pancreas (HE staining) were observed under light microscope. Positioning of DAPI labeled bmMSCs in vivo were detected under fluorescence microscope at the same time. The pancreas in SAP group showed significantly massive hemorrhage, edema, inflammation, and necrosis compared with control group. The inflammation, edema, hemorrhage and necrosis in each model of pancreatitis were reduced significantly in SAP+bmMSCs group as compared to SAP group (P<0.05). In bmMSCs transplanted group, bmMSCs remarkably reduced the levels of proinflammatory cytokines (TNF-α, IL-6, and IL-1β), on the contrary increased the levels of anti-inflammatory cytokines (IL-10) in SAP rats. Infused bmMSCs through tail vein + intraperitoneal indicate a better recovery than through tail vein or intraperitoneal alone. Compared with intraperitoneal injection method, more bmMSCs were observed to be presented in pancreas when bmMSCs were injected through tail vein + intraperitoneal or tail vein injection. In a rat model of SAP, transplantation of bm-MSCs through tail vein + intraperitoneal significantly inhibits inflammation and decreases pancreatic injury secondary to SAP. It was a better method for pancreatitis.