Background Sepsis is a complex pathophysiologic process, which is the leading cause of death in the world. Many studies have revealed that Chinese medicine has shown tremendous advantages on the treatment of sepsis. Our study aims to explore the effect of Huanglian jiedu decoction and Jiawei huanglian jiedu decoction on organ function in septic rats. Methods SD rats were randomly divided into 7 groups, sham-group, cecal ligation and puncture group (CLP, 18h/72h), Jiawei huanglian jiedu decoction group (JW, 18h/72h), Huanglian jiedu decoction group (W, 18h/72h). Except the Sham group, the rats in other groups received cecal ligation and puncture method to induce sepsis. CLP groups were intragastric administration with normal saline after CLP. Huanglian jiedu decoction and Jiawei huanglian jiedu decoction groups were intragastric administration with Huanglian jiedu decoction and Jiawei huanglian jiedu decoction in the same time points. Glutamic - pyruvic transaminase (ALT), glutamic oxalacetic transaminase (AST), total bilirubin (TBIL), creatinine(Cr), urea, creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH) were detected by biochemical analyzer. Brain natriuretic peptide (BNP), surfactant protein A (SP-A), chemotactic factor for monocyte-1 (MCP-1), D-lactic acid (D-LAC), complement 5a, mobility group box-1 protein B1(HMGB-1), interleukin 6 (IL-6) were analyzed by enzyme-linked immunosorbent assay (ELISA). Total lung capacity (TLC) and function residual capacity (FRC) were measured by buxco research system. The wet to dry weight ratio (W/D) was tested. Moreover, changes in tissue pathology were evaluated using hematoxylin and eosin (H&E) staining and electron microscope. Results The level of AST/ALT in serum was decreased after treatment with Huanglian jiedu decoction and Jiawei huanglian jiedu decoction. Moreover, the level of TLC and FRC was significantly increased, and the level of SP-A, W/D was significantly decreased. In addition, the level of CK-MB, IL-6, HMGB-1 and MCP-1 in serum was decreased. Inflammation factors were positively correlated with lung function, and the cardiac function was positively correlated with the organ function, the differences were statistically significant. In addition, the histological alterations of myocardium, lung and intestine were attenuated after treatment with Huanglian jiedu decoction and Jiawei huanglian jiedu decoction. Conclusion Huanglian jiedu decoction and Jiawei huanglian jiedu decoction can inhibit the inflammatory infiltration of septic rats and improve organ function.