The zygomatic nerve (ZN), which originates from the maxillary nerve at the pterygopalatine fossa, enters the orbit through the inferior orbital fissure. Within the lateral region of the orbit, the ZN divides into the zygomaticofacial (ZF) and zygomaticotemporal (ZT) nerves. The ZF and ZT nerves then pass on to the face and temporal region through the zygomaticoorbital foramen and enter their own bony canals within the zygomatic bone. However, multiple zygomaticofacial and zygomaticotemporal canals (ZFCs and ZTCs, respectively) can be observed, and their detailed intrabony courses are unknown. The aim of this study was clarify the three-dimensional intrabony courses and running patterns of the ZFCs and ZTCs, both to obtain a detailed anatomical description and for clinical purposes. Fourteen sides of the zygomatic bones were scanned as two-dimensional images using a micro-computed tomography (CT), with 32-μm slice thickness. Intrabony structures of each canals were three-dimensionally reconstructed and analyzed using Mimics computer software (Version 10.01; Materialise, Leuven, Belgium). We found that some ZTC was originated from ZFC. In 71.4% of the specimens, the ZTC(s) divided from the intrabony canal along the course of the ZFC(s). In other cases, 28.6% of ZTCs were opened through each corresponding ZT foramen. Zygomaticofacial canal originates from zygomaticoorbital foramen, divided into some of ZTCs, and is finally opened as ZF foramen. This new anatomical description of the intrabony structures of the ZFC(s) and ZTC(s) within the zygomatic bone by micro-CT technology provided helpful information to surgeons performing clinical procedures such as Le Fort osteotomy and reconstructive surgeries in the midface region.