Infestation of young apple fruits by the larvae of the peach fruit moth, Carposina sasakii Matsumura (Lepidoptera: Carposinidae), was studied by a small dedicated micro-magnetic resonance imaging (MRI) apparatus using the three-dimensional (3D) gradient-echo method and the two-dimensional (2D) and 3D spin-echo methods. Changes from a young larva at 1.8 mm in length to a mature one ready to leave the fruit were observed in relation to the progression of infestation of the fruit tissues. The trace of larva intrusion was demonstrated by a series of sliced images in the 3D image data of an infested fruit, where it entered from outside the calyx, and migrated to near the vasculature around the carpel through the core. The small, dedicated MRI device was proven useful for ecological studies of the growth and movement of insect larvae in their food fruits. It can also be applied to detect the infestation of small fruits by insect larvae.