A magnetic resonance imaging (MRI) water-fat separation method includes acquiring in-phase image raw measurement data and out-of-phase image raw measurement data with an MRI device, reconstructing an in-phase image and an out-of-phase image according to a system matrix and the raw measurement data using the penalty function regularized iterative reconstruction method, and calculating water and fat images according to the in-phase image and the out-of-phase image. The use of the penalty function regularized iterative method eliminates the need for k-space raw measurement data with a 100% sampling rate, thereby reducing the MRI scan time, shortening the entire imaging time, and improving the efficiency of the MRI device.