Oscillatory electroencephalographic (EEG) activity is associated with the excitability of cortical regions. Visual feedback of EEG-oscillations may promote sensorimotor cortical activation, but its spatial specificity is not truly guaranteed due to signal interaction among interhemispheric brain regions. Guiding spatially specific activation is important for facilitating neural rehabilitation processes. Here, we tested whether users could explicitly guide sensorimotor cortical activity to the contralateral or ipsilateral hemisphere using a spatially bivariate EEG-based neurofeedback that monitors bi-hemispheric sensorimotor cortical activities in the alpha band for healthy participants. Two different motor imageries (shoulder and hand MIs) were selected to see how differences in intrinsic corticomuscular projection patterns might influence activity lateralization. We showed alpha-band SMR-ERD during shoulder, but not hand MI, can be brought under ipsilateral control with guided EEG-based neurofeedback. These results are compatible with neuroanatomy; shoulder muscles are innervated bihemispherically, whereas hand muscles are mostly innervated contralaterally. We demonstrate the neuroanatomically-inspired approach enables us to investigate potent neural remodeling functions that underlie EEG-based neurofeedback via a BCI.