The intertwined connections between brain and body health are gaining increasing attention. Particularly, cardiovascular health interacts with cognitive and psychological health in complex ways. Yet, little is known about the phenotypic and genetic links of heart-brain systems. Using cardiac and brain magnetic resonance imaging (CMR and brain MRI) data from over 40,000 UK Biobank subjects, we developed detailed analyses of the structural and functional connections between the heart and the brain. CMR measures of the cardiovascular system were strongly correlated with brain basic morphometry, structural connectivity, and functional connectivity. The effects of cardiovascular risk factors on the brain were partially mediated by cardiac structures and functions. Genome-wide association study identified colocalizations with a wide spectrum of heart and brain diseases. Overall, our study illustrate that multi-system analysis using biobank-scale data may provide insights for inter-organ pathophysiological mechanisms and prevention and early detection of brain diseases.