In a magnetic resonance (MR) method and apparatus for implementing fat-water separation, MR data acquired representing one in-phase image and two out-of-phase images, phase differences between the two out-of-phase images are calculated, and the phases caused by the inhomogeneity of a magnetic field in the two out-of-phase images are calculated by using the phase differences; correcting linear phase differences in the in-phase image caused by eddy currents, by using the two corrected out-of-phase images. Calculations are then made on the basis of the three corrected images to obtain water and fat images. This method and apparatus effectively eliminate the adverse effects caused by the eddy currents in the currently available implementing process of the three points Dixon method.