An apparatus and method for reconstructing multi-spectral 3D MR images includes a magnetic resonance (MRI) apparatus that includes an MRI system having a plurality of gradient coils positioned about a bore of a magnet, and an RF transceiver system and an RF switch controlled by a pulse module to transmit RF signals to an RF coil assembly to acquire MR images. The MRI apparatus also includes a computer programmed to acquire a plurality of three-dimensional (3D) MR data sets, wherein each 3D MR data set is acquired using a central transmit and receive frequency set to an offset frequency value that is distinct for each 3D MR data set. The computer is also programmed to simultaneously generate a composite image and a magnetic field map based on the plurality of 3D MR data sets.