Accumulating evidence suggests that probiotics affect the microbial-gut-brain axis in a way that can prevent and treat Alzheimer’s disease (AD). However, the mechanism underlying the therapeutic effects still needs to be further investigated. This study aimed to examine the alleviating effect of Lacticaseibacillus paracasei L9 and Bifidobacterium animalis subsp. lactis A6 and possible mechanism in mice with AD. In this study, the administration of probiotics L9 and A6 effectively improved memory and learning functions in AD mice. The hippocampal cells of mice were partly recovered in morphology and rearranged more neatly after probiotics intervention. Meanwhile, L9 and A6 exhibited inhibitory effects on the phosphorylation of Tau and the deposition of Aβ, which were mediated via GSK-3β and PP2A kinases. Meanwhile, by metagenomic sequencing, we found interventions with L9 and A6 altered the intestinal microbiome’s taxonomic composition, reduced the abundance of pathogenic Desulfovibrio genera, and increased beneficial Clostridium and Paramuribaculum genera abundance. The fatty acids metabolism and biosynthesis of gut microbiome were also enhanced. Serum untargeted metabolomics also showed noticeable alternation in lipid-related metabolites, which may alleviate the pathogenesis of AD. These results revealed a mitigating role for probiotic L9 and A6 in AD prevention and offer new insights into AD prevention via gut-brain connection.