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Blood stasis syndrome (BSS) is characterized by blood retardation and is the major cause of some deadly diseases. Some factors that affect BSS have been identified. However, the small molecule that related to BSS is still largely unknown. Traditional Chinese Medicine (TCM), such as Sanleng and Ezhu, has been used for a long time in treating BSS and promising outcomes have been achieved. However, the mechanism of how they work is unclear. Thus, we constructed the Rat BSS model and treated them with Sanleng and Ezhu. Then, the liver dialysis of those rats was collected and the small molecule metabolites were analyzed by GC-MS based metabolomics approach. Our results showed after Sanleng and Ezhu treatment, several small molecule metabolites were significantly changed metabolites (VIP1 and P0.05). Pathway enrichment analysis also showed that Sanleng and Ezhu share the similar mechanism in treating BSS, such as regulating Glyoxylate and dicarboxylate metabolism pathway and energy metabolism. Besides, we also identified some key metabolites that were significantly correlated with BSS. In conclusion, those findings uncover the mechanism of Sanleng and Ezhu in treating BSS.