A method of magnetic resonance imaging (MRI) includes applying radio frequency (RF) pulses including a plurality of frequency components and a selection gradient to a target to simultaneously excite a plurality of sub-volumes included in each of a plurality of groups, wherein neighboring sub-volumes of all sub-volumes constituting a volume of the target belong to different groups; acquiring magnetic resonance signals from the plurality of sub-volumes by performing 3D encoding on each of the excited sub-volumes; and reconstructing the acquired magnetic resonance signals into image data corresponding to each of the plurality of sub-volumes.