A magnetic resonance apparatus of the present embodiment includes: a gantry which includes a static field magnet, a gradient coil and an RF coil to image an object; processing circuitry; a memory that stores processor-executable instructions that, when executed by the processing circuitry, cause the processing circuitry to detect at least one position of an aortic valve and a pulmonary valve from three-dimensional image data including a heart of the object, as at least one characteristic region inside the heart, specify a position of an imaging cross-section substantially orthogonal to a bloodstream path inside the heart based on the position of the aortic valve or the pulmonary valve, and cause the gantry to image the imaging cross-section of the object at the specified position of the imaging cross-section.