Objective This paper investigated the effects of the moderate-intensity treadmill exercise on microarchitecture of trabecular bone in ovariectomized (OVX) rats by micro-CT. Methods Thirty female SD rats were randomly divided into following three groups: sham-operation (Sham), ovariectomized (OVX), and ovariectomized exercised (EX, 18 m/minute, 45 min/day, 5 uphill, 4 times/week). At 14wk of the regular exercise treatment, the lumbar vertebrae BMD were detected by DEXA. Micro-CT scanning and three-dimensional structure reconstruction were used to analyze the microarchitecture of the third lumbar vertebrae and bonebiomechanical test was carried on the fourth lumbar vertebrae. Results Compared with the OVX group, the BMD of second lumbar vertebrae, the maximum load, maximum stress, and elastic modulus in third lumbar vertebrae, as well as the volume and number of trabecular bone in fourth lumbar vertebrae were significantly higher in EX group whereas the space of trabecular bone was significantly lower. There were no significant differences in the thickness of trabecular bone. Conclusion The moderate-intensity treadmill exercise could benefit the microarchitecture of lumbar vertebra in OVX rats.