Ptychographic X-ray computed tomography (PXCT) is a quantitative imaging modality that non-destructively maps the 3D electron density inside an object with tens of nanometers spatial resolution. This method provides unique access to the morphology and structure of the osteocyte lacuno-canalicular network (LCN) and nanoscale density of the tissue in the vicinity of an osteocyte lacuna. Herein, we applied PXCT to characterize the lacunae and LCN in a male Wistar rat model of glucocorticoid-induced osteoporosis (GIO). The ptychographic images revealed significant (p < 0.05) differences in the number of canaliculi originating from the lacuna per ellipsoidal surface unit, Ca.Nb (p = 0.0106), and the 3D morphology of the lacuna (p = 0.0064), between GIO and SHAM groups. Moreover, the mean canalicular diameter, Ca.Dm, was slightly statistically un-significantly smaller in GIO (152 ± 6.5) nm than in SHAM group (165 ± 8) nm (p = 0.053). Our findings indicate that PXCT can non-destructively provide detailed, nanoscale information on the 3D organization of the LCN in correlative studies of pathologies, such as osteoporosis, leading to improved diagnosis and therapy.