A system and method for generating MR phase contrast images near metal include an MRI apparatus that includes an MRI system having a plurality of gradient coils and an RF transceiver system and an RF switch controlled by a pulse module to transmit RF signals to an RF coil assembly. The MRI apparatus also includes a computer programmed to acquire a plurality of three-dimensional (3D) MR data sets and to generate a plurality of frequency images based on the plurality of 3D MR data sets. Each 3D MR data set is acquired using a central transmit frequency and a central receive frequency set to an offset frequency value that is distinct for each 3D MR data set. The computer is also programmed to convert the plurality of frequency images to a plurality of time domain images and to generate a phase image based on the plurality of time domain images.