Osteoporosis is a major disease in aged women, increasing the risk for fractures accompanied by changes in the microarchitecture. The aim of this study was to investigate the three-dimensional (3D) histomorphology of femur diaphysis in the animal model for postmenopausal osteoporosis. The cortical bone of femur diaphysis of the rat was serially sectioned at a thickness of 5 µm and evaluated age-associated changes of the intracortical (osteonal) canal networks three-dimensionally. Cortical microstructures of 10-month old rats were not affected by ovariectomy. Intracortical canal networks were radial toward endosteal aspect and frequently interconnected across the neighboring canals with short arciform and irregular canals reminiscent for resorption spaces in ovarectomized 16-month old rats, contrary to intact canals in 16-month old control rat. Increased proportion of the periosteal circumference lamella and deformed endosteal regions with rare cortical canals hampered reconstructive histomorphology in ovarectomized rats of 26 month age. We have shown that 3D reconstruction of rat femur of the aged model over 16-month old is suitable methods that evaluate and microstructural change of the intracortical canals and cortical bone porosity by estrogen depletion.