A magnetic resonance imaging (MRI) method includes: applying radio-frequency (RF) pulses comprising a plurality of frequency components and a selection gradient to a subject to simultaneously excite a plurality of sub-volumes in each of a plurality of groups, wherein a plurality of sub-volumes making up a volume of the subject are divided into the plurality of groups so that any neighboring sub-volumes belong to different groups; performing three-dimensional (3D) encoding on each of the excited sub-volumes using a plurality of encoding methods; acquiring magnetic resonance signals from the encoded sub-volumes; and reconstructing the acquired magnetic resonance signals into image data corresponding to each of the encoded sub-volumes.