Objective To investigate the effect of whole body vibration training on biomechanics and Wnt3a protein expression of the femur. Methods Forty-eight female SD rats were randomly divided into sham operation group, osteoporosis group and whole body vibration group, 16 in each group. The bone morphometric parameters were measured by Micro-CT, mechanical parameters of bone structure and materials were measured by three-point bending test, protein expression of Wnt3a and β-catenin was measured by Western blotting, and gene expression of Wnt3a, β-catenin, cyclin D1 and tcf1 was detected by qRT-PCR. ResultsCompared with sham operation group, bone mineral density (BMD), bone volume fraction (BVF), trabecular number, trabecular thickness and cortical bone thickness in osteoporosis group were decreased, and trabecular space was increased; compared with osteoporosis group, BMD, BVF, trabecular number, trabecular thickness and cortical bone thickness in whole body vibration group were increased, and trabecular space was decreased. Compared with sham operation group, the maximum load, elastic load and deflection of osteoporosis group were significantly reduced; compared with osteoporosis group, the maximum load, elastic load and deflection of whole body vibration group were significantly increased. Compared with sham operation group, the maximum stress, elastic stress, maximum strain and elastic modulus in osteoporosis group decreased significantly; compared with the osteoporosis group, the elastic stress, maximum strain and elastic modulus in whole body vibration group increased significantly. Compared with sham operation group, Wnt3a, β-catenin protein and gene expression decreased, cyclin D1, tcf1 gene expression also decreased; compared with osteoporosis group, Wnt3a, β-catenin protein and gene expression increased, cyclin D1, tcf1 gene expression increased as well. Conclusions Whole body vibration training can improve biomechanical properties of the femur and expression of Wnt3a protein in osteoporotic rats. The research findings provide laboratory reference data for the prevention and treatment of osteoporosis by whole body vibration training.