Background: Sepsis, a systemic inflammatory disease that leads to life-threatening organ functions disorders, such as liver and kidney injury. Ulinastatin (UTI) and Thrombomodulin (TM) are active macromolecules isolated from human urine. UTI and TM have been found to have therapeutic effects on inflammatory diseases. In this study, we verified protective effect of UTI combined with TM on liver and kidney injury caused by sepsis, and further explored the mechanisms.Methods: The sepsis model was established by intravenous injection of LPS into the tail vein of rats. Blood, liver and kidney tissues were collected after injection of UTI or TM. ELISA was used to measure serum levels of pro-inflammatory cytokines. The characteristic functional indexes of liver and kidney in serum and multiple coagulation function indexes of rats were detected via corresponding kits. Histological changes of liver and kidney tissues were investigated by HE staining. Apoptosis in liver and kidney tissues were examined by TUNEL staining, and the expression levels of apoptosis-related proteins were also analyzed. HMGB1/TLR4/NF-κB pathway in liver and kidney tissues were examined by Western Blot. PCNA-positive cells were detected by immunohistochemistry. The survival rate of rats in each group was statistically analyzed.Results: UTI combined with TM reduced LPS-induced secretion of IL-6 and TNF-α in the serum. The drug combination reduced the liver and kidney functional indicators ALT, AST, BUN and Cr, and ameliorated liver and kidney pathology injury of rats. It inhibited apoptosis of liver and kidney cells via down-regulating the expression of apoptotic protein Bax, Cleaved caspase-3, up-regulating the expression of anti-apoptotic protein bcl-2, and promoted the proliferation of liver and kidney cells. The drug combination reversed the up-regulation of HMGB1, TLR4, and phosphorylated NF-κB protein mediated by LPS. Anticoagulation test indicated UTI does not affect the anticoagulant effect of TM when they are used in combination. Moreover, the drug combination significantly improved the survival rate of septic rats. Conclusions: These results indicate that UTI combined with TM plays a key role in protecting liver and kidney injury in septic rats, which will suggest a promising treatment for sepsis-induced organ injury.