Hypertension is one of the main risk factors for vascular dementia and Alzheimer disease. To predict the onset of these diseases, it is necessary to develop tools to detect the early effects of vascular risk factors on the brain. Resting-state functional magnetic resonance imaging can investigate how the brain modulates its resting activity and analyze how hypertension impacts cerebral function. Here, we used resting-state functional magnetic resonance imaging to explore brain functional-hemodynamic coupling across different regions and their connectivity in patients with hypertension, as compared to subjects with normotension. In addition, we leveraged multimodal imaging to identify the signature of hypertension injury on the brain. Our study included 37 subjects (18 normotensives and 19 hypertensives), characterized by microstructural integrity by diffusion tensor imaging and cognitive profile, who were subjected to resting-state functional magnetic resonance imaging analysis. We mapped brain functional connectivity networks and evaluated the connectivity differences among regions, identifying the altered connections in patients with hypertension compared with subjects with normotension in the (1) dorsal attention network and sensorimotor network; (2) dorsal attention network and visual network; (3) dorsal attention network and frontoparietal network. Then we tested how diffusion tensor imaging fractional anisotropy of superior longitudinal fasciculus correlates with the connections between dorsal attention network and default mode network and Montreal Cognitive Assessment scores with a widespread network of functional connections. Finally, based on our correlation analysis, we applied a feature selection to highlight those most relevant to describing brain injury in patients with hypertension. Our multimodal imaging data showed that hypertensive brains present a network of functional connectivity alterations that correlate with cognitive dysfunction and microstructural integrity. Registration- URL: https://www.clinicaltrials.gov; Unique identifier: NCT02310217.