The MRI apparatus includes: a radio frequency (RF) transmitter configured to transmit an RF signal including multiple frequency signals corresponding respectively to multiple slices of an object to excite the multiple slices of the object; a gradient amplifier configured to apply a three-dimensional (3D) spatial encoding; an RF receiver configured to receive MR signals in an overlapped state from the multiple slices in a same repetition time (TR) period; and an image processor configured to acquire 3D k-space data based on the MR signals and acquire an MR image of each of the multiple slices based on the 3D k-space data.