A magnetic resonance imaging (MRI) apparatus and a control method thereof are provided. The MRI apparatus includes a scanner, and a controller configured to control the scanner to receive magnetic resonance (MR) signals corresponding to a magnitude of a y-axis gradient magnetic field in a respiration cycle of a patient, each of the MR signals being received at a time interval equal to a time period of the respiration cycle over a number of the received MR signals. The MRI apparatus further includes a processor configured to extract an MR signal received in a respiration condition of the patient from the received MR signals, fill a k-space with the extracted MR signal, and generate an MR image by reconstructing data of the filled k-space.