The vibration attenuation mechanism of shear thickening fluid- (STF-) filled sandwich structures was investigated in this study. Structural equivalent damping, stiffness, and mass increased simultaneously with the increase in the volume fraction of shear thickening fluid. However, the damping ratio decreased and natural frequency increased with the increase in structural mass. Thus, the damping ratio was not a monotonically increasing function of the volume fraction of STF. A modified shear strain model of the damping layer was developed based on the following conditions: (1) under the condition of small strain, shear thickening fluid was regarded as linear viscoelastic material, and (2) the warpage of the sandwich beam was considered during deformation and the influence of STF on the shear strain of sandwich beam. According to the modified shear strain model of the damping layer, the shear thickening occurred at 1 Hz to 20 Hz during vibration. Therefore, the resonance point of the structure shifted to the left. The predictions were in excellent agreement with the experimental results. The results demonstrated that shear thickening fluid improved the vibration damping performance of the sandwich structure, while the thickening ability was not the higher, the better.