A method and apparatus for generating a magnetic resonance image including applying to a target first radio frequency (RF) pulses having phases and different frequencies to excite a plurality of sub-volumes constituting a volume of the target, and acquiring first magnetic resonance signals from the plurality of sub-volumes, and applying to the target second RF pulses having the same frequencies as the frequencies of the first RF pulses and phases at least one of which is different from the phases of the first RF pulses, and acquiring second magnetic resonance signals from the plurality of sub-volumes. Also, data may be generated based on the first and second magnetic resonance signals.