In this paper, a fully time-domain coupling method of the discrete element method (DEM) combination with multi-flexible body dynamics (MFBD) was proposed to investigate the particle motion and vibration reduction as well as energy dissipation characteristics of flexible vibration structure coupling with particle damping under transient free vibration and random excitation conditions. The transient free vibration and random vibration reduction experiments of flexible vibration cantilever beam with particle damping were carried out. In addition, the influence of particle diameter and filling rate on the vibration reduction characteristics is further analyzed. Results show that the proposed DEM-MFBD coupling method is well verified by experiments. The particle motion process under free vibration condition can be manifested as three typical motion states, namely, the double-side particle–container collision, the single-side particle–container collision, and no collision. The vibration energy is mainly dissipated in the first state. Under random vibration excitation, the maximum energy dissipation of particle damping mainly occurs at the natural frequency, and the vibration reduction mechanism of particle damping is mainly attributed to the particle–particle energy dissipation.