Moisture migration of fresh‐cut apple during 4 °C storage was monitored by low‐field nuclear magnetic resonance (LF‐NMR) and magnetic resonance imaging (MRI). Three water components were identified in apple tissue by LF‐NMR T2 relaxation, corresponding to water in cell wall, cytoplasm and vacuole. The relaxation results also revealed that the moisture migrated from the vacuole to cytoplasm and the mobility of water in vacuole decreased with the extension of storage time. T2 weighted images of MRI indicated that high density of water appeared at the edge of the fresh‐cut apple in the later stage of storage. Breakdown of cell walls and intracellular network were observed by cryo scanning electron microscope (cryo‐SEM). Moreover, storage process also led to the decrease in moisture content, browning and softening of fresh‐cut apple. In addition, good prediction models have been developed for quality indicators using partial least squares regression based on Carr–Purcell–Meiboom–Gill decay data.