Neurodegenerative diseases (NDs), mainly including Alzheimer’s disease, Parkinson’s disease, and multiple sclerosis, represent a major public health challenge with the steady increase of aging population worldwide. Emerging evidence has revealed the key role of the microbiota-gut-brain axis in the pathogenesis of NDs. Diet is one of the most important environmental factors shaping the structure and function of gut microbiota. Manipulating the gut microbiota through specific diet patterns may represent a promising approach for NDs prevention. In this review, we highlight gut microbiota variations in NDs, outline several crucial signaling pathways of the gut-brain communication, and discuss the interplay of nutrients-microbes and biological effect of diet-derived microbial metabolites on neural physiology. In particular, we summarized the current knowledge about the application of dietary patterns in NDs to prevent disease progression via the modulation of the gut microbiota. Our study provides novel insights on the diet-microbiota-gut-brain axis in neurodegenerative disorders and highlights the potential of developing microbiome-targeted personalized dietary intervention for NDs management.