Objective To investigate the effects of CoQ10 on trabecular microstructure and biomechanical properties of femur in a rat model of bone loss induced by ovariectomy and to compare the effects of CoQIO and Estradiol Valerate. Methods 48 three- month-old female Sprague-Dawley rats were randomly divided into 6 groups (n = 8 per group) which were Sham, OVX, WGO, WGO + CoQ10 (high dose, low dose) and EV. The bone loss model had ovariectomy surgery. The femoral epiphysis end (FED) was analyzed by micro-CT and three-dimensional reconstructions. Results Micro-CT data showed that bone volume/total volume (BV/TV),trabecular number (Tb. N), trabecular thickness (Tb. Th) and trabecular bone mineral density (BMD) in the OVX group were significantly lower than those in the sham group; whereas the trabecular separation (Tb. Sp) and structure model index (SMI) were significantly greater in the OVX group than those for the sham group. Biomechanical properties including maximum strength, break strength, break strain and stiffness decreased significantly in the OVX group. Compared with the OVX group, the micro-CT data showed that trabecular microstructure was well repaired in the Estradiol Valerate group, with several parameters of the biomechanical properties (maximum strength,break Strength, break strain and stiffness) significantly improved. In the Coql0 group, the biomechanical properties were significantly improved, and several of the micro-CT data (Tb. N, Tb. Sp, SMI and BV/ TV) were well repaired. Conclusion Compared with OVX, CoQ10 could greatly improve the trabecular microstructure as well as the biomechanical properties of femur in a rat model of osteoporosis induced by ovariectomy. CoQ10 may have great potential in the prevention of osteoporosis.