A magnetic resonance imaging apparatus comprises: a chemical shift data storage unit, a first frequency adjusting unit, a first imaging unit, a second frequency adjust unit and a second imaging unit. The chemical shift data storage unit stores chemical shift data. The first frequency adjusting unit adjusts a center frequency of a first excitation pulse to a resonant frequency of a designated first substance. The first imaging unit generates an image in which the first substance is enhanced by performing a chemical shift imaging scanning with the first excitation pulse. The second frequency adjust unit automatically adjusts a center frequency of a second excitation pulse to a resonant frequency of a preliminarily designated second substance in accordance with chemical shift data. The second imaging unit generates an image in which the second substance is enhanced by performing a chemical shift imaging scanning with the second excitation pulse.