In a multi-channel magnetic resonance imaging reconstruction method for water-fat separation, one in-phase image and two opposed-phase images are acquired with multiple reception coils in respective channels. The sensitivity distribution of the coils of the respective channels is calculated. The images of respective channels are merged dependent on the sensitivity distribution. A phase difference between the two opposed-phase images is calculated. At lease one characteristic region of the in-phase image is detected, which is used as a criterion for phase correction. The phases of the opposed-phase images are corrected and images of water and fat are calculated. The method provides stable and reliable imaging, has a short reconstruction time and also solves the problem that images of water and fat may be exchanged.