This study examined nondestructive analysis of internal quality characteristics and physical changes in fresh agricultural products using magnetic resonance imaging (MRI) and evaluated its potential as a quality assessment tool. Korean melons, pears, and onions were selected, and changes in internal tissues, damage, and heterogeneity were qualitatively analyzed. After seven days of storage, moisture was redistributed from the flesh to the peel and stem-end regions in melon samples, resulting in increased signal intensity in the two regions on MRI. In pear samples, normal tissues exhibited strong and uniform signal intensity during storage, whereas damaged tissues showed reduced signal intensity and enlarged abnormal regions, owing to moisture loss and tissue degradation, respectively. In onion samples, the signal intensity of the central sprouting region was approximately twice than that of the surrounding shell tissue, and the outer shell tissue exhibited higher signal intensity than the inner shell tissue due to magnetic susceptibility. These results demonstrate that MRI can evaluate the internal quality of fresh agricultural products in a nondestructive manner and grade them objectively, suggesting broad application potentials in agro–food science field.