The magnetic resonance imaging apparatus includes a main magnet to generate a static magnetic field in an imaging region, a gradient coil assembly to form a gradient in the static magnetic field, a radio frequency (RF) coil assembly to apply a first RF pulse and second RF pulse with respect to n (n≧2) slice regions located at different positions in the imaging region, to excite atomic nuclei of the slice regions, and a controller to control the RF coil assembly to apply a first RF pulse and second RF pulse having a first center frequency f0 to a first slice and to apply a first RF pulse having a second center frequency f0+fs1 and a second RF pulse having a third center frequency f0−fs1 to a second slice.