Alcohol abuse damages the brain and triggers cognitive impairment. Intestinal dysbiosis has recently been shown to be involved in psychiatric disorders, which suggests the possibility of intestine-to-brain interactions in the development of alcohol abuse. In this study, chronic intermittent alcohol exposure (CIAE) model was established in C57BL/6 male mice and the spatial memory were detected by Barnes maze (n = 16/group). The fecal microbiota and its metabolites were detected by 16S rDNA sequencing and non-target liquid chromatograph mass spectrometer (LC-MS) (n = 8/group). Effects of alcohol on intestinal barrier and blood-brain barrier (BBB) permeability were detected by Evens blue leakage assay (n = 4/group), and the activation state of microglia and TLR4 expression were conducted by immunofluorescence co-localization (n = 4/group). The morphological changes of microglia were analyzed with Image J Analyze Skeleton software, and the protein levels of TLR4 and inflammatory factors were detected by Western Blot (n = 8/group). Results indicated that alcohol alters the components of fecal microbiota and metabolites, and damages the intestinal barrier and BBB, leading to spatial memory impairment in mice. By giving mice specific prebiotics (n = 16/group), we pointed out that increased endotoxin coming from Gram negative bacteria such as lipopolysaccharides (LPS) cross the BBB to activate microglia and inflammatory pathways in the prefrontal cortical (PFC) and hippocampus (HIP), releasing inflammatory factors and resulting in neuroinflammation. Thus, the fecal microbiota seems to be a potential target in the management of alcoholic brain disease.