The functional aspects of mast cell-microglia interactions are important in neuroinflammation. Our previous studies have demonstrated that mast cell degranulation can directly induce microglia activation. However, the role of mast cells in Lipopolysaccharide (LPS)-induced microglia activation, neuroinflammation and cognitive impairment has not been clarified. This study investigated the interaction between brain microglia and mast cells through site-directed injection of cromolyn into rat right hypothalamus using stereotaxic techniques. Cognitive function was subsequently assessed using trace fear conditioning and Y maze tests. Mast cells in rat brain were stained with toluidine blue and counted using Cell D software. Microglia activation was assessed by Iba1 immunohistochemistry both in rat brain and in mast cell-deficient Kit mice. Receptor expression in rat microglia was determined using flow cytometry analysis. Cytokine levels in rat brain tissue and cell supernatant were measured using high-throughput ELISA. Western blotting was used to analyze Cell signaling proteins. In this study, intraperitoneal injection of 1 mg/kg LPS induced mast cell activation in hypothalamus and cognitive dysfunction in rats, and that this process can be repressed by the mast cell stabilizer cromolyn (200 μg). Meanwhile, in mice, LPS IP injection induced significant microglia activation 24 h later in the hypothalamus of wild-type (WT) mice, but had little effect in Kit mice. The stabilization of mast cells in rats inhibited LPS-induced microglia activation, inflammatory factors release, and the activation of MAPK, AKT, and NF-κB signaling pathways. We also found that LPS selectively provokes upregulation of H R, H R, PAR2, and TLR4, but downregulation of H R and H R, in ipsilateral hypothalamus microglia; these effects were partially inhibited by cromolyn. In addition, LPS was also found to induce activation of P815 cells , consistent with findings from experiments. These activated P815 cells also induced cytokine release from microglia, which was mediated by the MAPK signaling pathway. Taken together, our results demonstrate that stabilization of mast cells can inhibit LPS-induced neuroinflammation and memory impairment, suggesting a novel treatment strategy for neuroinflammation-related diseases.