This study aimed to provide topographic information of the greater occipital (GON) and third occipital (3ON) nerves, with the three-dimensional locations of their emerging points on the back muscles (60 sides, 30 cadavers) and their spatial relationship with muscle layers, using a 3D digitizer (Microscribe G2X, Immersion Corp, San Jose CA, USA). With reference to the external occipital protuberance (EOP), GON pierced the trapezius at a point 22.6 ± 7.4 mm lateral and 16.3 ± 5.9 mm inferior and the semispinalis capitis (SSC) at a point 13.1 ± 6.0 mm lateral and 27.7 ± 9.9 mm inferior. With the same reference, 3ON pierced, the trapezius at a point 12.9 ± 9.3 mm lateral and 44.2 ± 21.4 mm inferior, the splenius capitis at a point 10.0 ± 5.3 mm lateral and 59.2 ± 19.8 mm inferior, and SSC at a point 11.5 ± 9.9 mm lateral and 61.4 ± 15.3 mm inferior. Additionally, GON arose, winding up the obliquus capitis inferior, with the winding point located 52.3 ± 11.7 mm inferior to EOP and 30.2 ± 8.9 mm lateral to the midsagittal line. Knowing the course of GON and 3ON, from their emergence between vertebrae to the subcutaneous layer, is necessary for reliable nerve detection and precise analgesic injections. Moreover, stereotactic measurement using the 3D digitizer seems useful and accurate for neurovascular structure study.