Objective To study changes in bone microstructure of osteoporotic rats by multiscale analysis. Methods A total of 20 5-month-old female SD rats were randomly divided into two groups, i.e., ovariectomy (OVX) group (n=12) and the SHAM group (n=8), respectively. The rats in OVX group were subjected to bilateral ovariectomy and became osteoporosis models after 8 weeks, while sham operation was performed for the SHAM group. Changes in microstructure of cortical bone and cancellous bone at tissue scale, and osteocyte lacunar-canalicular network (LCN) and extracellular matrix (ECM) at cell scale were quantitatively analyzed using Micro-CT and SR-Nano-CT. Results At tissue scale, the cross-sectional area of cortical bone in OVX group was significantly higher than that in SHAM group (P<0.05), and the bone mineral density (BMD) and thickness of cortical bone were not significantly different from those in SHAM group. The trabecular BMD, bone volume fraction, trabecular thickness and trabecular number in OVX group were significantly decreased in comparison with SHAM group (P<0.01), while the trabecular separation was significantly increased (P<0.01). At cell scale, there was no significant difference in the semiaxes of lacunae between OVX group and SHAM group, but the thickness of lacunae and the diameter of canaliculi in OVX group were significantly increased in comparison with SHAM group (P<0.05). At the same time, the porosity of cortical bone in OVX group was significantly higher than that in SHAM group at cell scale (P<0.05). Conclusions The bone microstructure in OVX group varied to different extents at tissue and cell scales. At tissue scale, the cancellous bone loss was severe, while the cortical bone had fewer changes. At cell scale, porosity of the lacunar-canalicular network significantly increased, which directly affected the BMD and strength of cortical bone. Multiscale analysis on changes in bone microstructure of OP rats has potential application value for clinical diagnosis and pathological analysis of osteoporosis.