Microbiota-gut-brain axis, a bidirectional communication, was proposed as an important role in Alzheimer’s disease (AD). However, the correlation between gut microbiota and brain microstructure in AD remained unclear. Triple-transgenic mouse models of AD were used to investigate brain-behavior-gut-microbiome interaction. Diffusion MRI, behavior tasks, and intestinal bacteria gene analysis were applied in this study. The findings implied that the altered brain microstructure and atypical distribution of gut microbiota were associated with the cognitive dysfunction in AD.