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Background The YiQi-HuoXue therapeutic approach, derived from traditional Chinese medicine, has long been used to invigorate Qi, promote blood circulation, and restore brain function in various neurological and cerebrovascular disorders. Despite its extensive clinical application, the therapeutic potential and underlying mechanisms of YiQi-HuoXue in sepsis-associated encephalopathy (SAE)—a neuroinflammatory condition with no effective treatment—remain insufficiently elucidated. Objective To test whether YiQi-HuoXue Prescription (YQHXP) mitigates SAE and to define a mechanism centered on endothelial VCAM-1 and microglial efferocytosis. Methods LPS-challenged mice received oral YQHXP and were assessed by Morris water maze (MWM) and open-field tests (OFT). Hippocampal tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and microglial activation were quantified by enzyme-linked immunosorbent assay (ELISA) and immunostaining. YQHXP constituents and plasma-exposed prototype constituents were profiled by UPLC-HRMS. Network pharmacology integrated with hippocampal RNA-seq nominated VCAM-1–efferocytosis nodes. In vitro , efferocytosis (PKH67 + /F4/80 + ), apoptosis, and cytokine release were measured, with pathway relevance probed using a MER proto-oncogene tyrosine kinase (MERTK) inhibitor (UNC2250) and a VCAM-1 suppressor (rutin). VCAM-1–ligand interactions were evaluated by docking and 100-ns molecular dynamics (MD) simulations, and binding was confirmed by surface plasmon resonance (SPR). Results YQHXP improved spatial learning and novelty-directed exploration, and reduced hippocampal TNF-α, IL-6, and microglial activation. Analyses converged on a VCAM-1–linked efferocytosis axis involving complement C1q subcomponent B (C1QB)/MERTK. YQHXP downregulated VCAM-1, upregulated C1QB and MERTK in hippocampus and BV2 cells, enhanced efferocytosis, and decreased microglial apoptosis and cytokine release. Rutin or YQHXP alone increased efferocytosis; YQHXP partially restored clearance under MERTK inhibition, consistent with VCAM-1–gated regulation. Docking/MD predicted VCAM-1 engagement by several plasma-exposed prototypes, and SPR confirmed sub-millimolar binding between VCAM-1 and ginsenoside Rg1. Discussion YQHXP may attenuate experimental SAE via VCAM-1–mediated enhancement of microglial efferocytosis, supporting VCAM-1 as a pharmacodynamic marker and efferocytosis as an actionable therapeutic axis.