Limited investigations have been carried out on the physiological and growth responses of bark to wounding, even though wound periderms play crucial roles in tree defenses. To understand the mechanisms of wound periderm formation, we studied the growth responses and structural changes of wounded bark of three Cryptomeria japonica individuals. We observed the developmental time frame and morphology of wound periderms around mechanically induced wounds in summer. The wound responses included discoloration, lignification, and suberization in tissues present at the time of wounding, followed by wound periderm formation and secondary metabolite deposition. The trees had developed wound periderms approximately 4 weeks after wounding. The wound periderms were within 3 mm in the axial directions and within 1 mm in the lateral directions from the wound surfaces. The distinct patterns of wound periderm formation in the axial and lateral regions resulted from the arrangement and anatomical features of the cells adjacent to the wounds. The wound phellem cells were tangentially narrower and axially shorter in the side and upper/lower regions, respectively, of the wounds. Therefore, the cell division frequencies in the planes parallel to the wound surface may be greater than those in the other directions. Wound reactions in bark might initially be triggered by microenvironmental changes, such as the spread of desiccation, which depends directly on the morphology of phloem cell complexes.