The invention discloses a gradient-echo multi-echo water and fat separation method. The method includes the following steps of 1, using a three-dimensional gradient-echo N echo sequence for conductingimaging scanning on a magnetic resonance imaging region, collecting N pieces of echo data, and using a GRAPPA technology for accelerating data collection during collection, wherein N is greater thanor equal to 4; 2, using the GRAPPA technology for fitting and restoring to-be-collected phase encoding data of the N pieces of echo data within respective K spaces, and then conducting preliminary data processing to obtain complete image domain data of N echoes; 3, substituting the image domain data of the N echoes into a water and fat separation algorithm of a multi-peak water-fat model, introducing T2* variables, conducting iterative calculation, obtaining a T2* distribution map of an imaged object, and meanwhile obtaining water and fat images through calculation. According to the method, the T2* distribution can be accurately estimated, the signal attenuation between the echoes is effectively corrected, and phase changes caused by inhomogeneity of a magnetic field are reduced, so that results of the quantitative analysis images are more accurate and stable. A magnetic resonance imaging system using the method is also provided.