Ochratoxin (OT) contamination of medicinal herbs is a serious threat to human health. This study was performed to investigate the mechanism of OT contamination of licorice (Glycyrrhiza sp.) root. Licorice root samples were cut into eight parts, which were placed separately on sucrose-free Czapek Dox agar medium, inoculated with the spores of ochratoxigenic Aspergillus westerdijkiae. After incubation for 10 and 20 days, the OT contents of the samples were determined by high-performance liquid chromatography, and microtome sections prepared from the samples were analyzed by desorption electrospray ionization tandem mass spectrometry, to visualize OT localization. The same sections were further examined by light microscopy and scanning electron microscopy, to investigate the path of fungal mycelial penetration of the inner roots. OT concentrations tended to increase from the upper- to the middle-root parts. OTs were located in cut areas and areas of cork layer damage; they were not present in the undamaged cork layer, indicating that the structure of this layer prevents OT contamination of the licorice root.