A method of controlling a magnetic resonance imaging (MRI) apparatus including performing, by the MRI apparatus, blipped-controlled aliasing parallel imaging (blipped-CAIPI) obtaining k-space data on a subject determining a phase error of a chemical shift component, wherein the phase error of the chemical shift component is proportional to a geometric error based on a resonant frequency difference between a main component and the chemical shift component in the subject comparing the k-space data with data in which the phase error of the chemical shift component is reflected, wherein the data in which the phase error of the chemical shift component is reflected is associated with data on the main component and data on the chemical shift component and determining final data for image restoration based on a result of the comparison.