Cognitive impairment is a significant concern in aging populations. This study utilized Mendelian randomization analysis to explore the impact of dietary habits and macro-nutrients on cortical structure. A bidirectional Mendelian randomization approach was employed, incorporating large-scale genetic data on dietary habits and brain cortical structure. The results did not reveal significant causal relationships between dietary factors and overall cortical structure and thickness. However, specific dietary factors showed associations with cortical structure in certain regions. For instance, fat intake affected six cortical regions, while milk, protein, fruits, and water were associated with changes in specific regions. Reverse analysis suggested that cortical thickness influenced the consumption of alcohol, carbohydrates, coffee, and fish. These findings contribute to understanding the potential mechanisms underlying the role of dietary factors in cognitive function changes and provide evidence supporting the existence of the gut-brain axis.