Understanding the mechanisms of motor imagery, the mental simulation of movement without execution, is key for the development of neurotechnologies, including understanding inter-individual variability in motor imagery performance. For instance, for detecting covert motor intent in noncommunicative patients or refining motor commands through brain-computer interfaces. While motor imagery engages motor-related brain regions, its precise mechanisms remain unclear, particularly in relation to cardiac dynamics. Evidence suggests heart-rate variability features have potential to enhance tasks’ classifications, yet the brain-heart relationship is not well understood. In this study, we examined motor imagery learning using a task involving right-hand grasping imagery. We found that motor imagery is correlated with a task-dependent modulation of cardiac sympathetic activity and its relation with directed functional connectivity from the supplementary motor area to premotor and primary motor cortices. Additionally, cerebellar-supplementary motor area segregation, in relation to cardiac parasympathetic activity, indexed longitudinal motor learning. These results suggest that dynamic reconfiguration of brain-heart interactions contributes to sensorimotor function and learning-related physiology during motor imagery, supporting the brain-heart axis as a functional component of motor imagery rather than a passive correlate.