In a method and magnetic resonance (MR) apparatus for heart diffusion imaging, when an ECG trigger signal by a computer that operates an MR scanner, the MR scanner is operated to acquire a navigator echo before a stimulated echo sequence, in order to detect diaphragm position information. When the first diaphragm position information is not located in an acquisition window, the stimulated echo sequence is not executed, and the computer waits to receive the next ECG trigger signal. The detection time of the navigator echo after the stimulated echo sequence as well as the acquisition time of the stimulated echo sequence, are thus eliminated when the first diaphragm position information does not meet requirements, so can significantly reduce scanning time, and increase the image SNR.