High temperature superconducting (HTS) magnetic levitation (maglev) train has the potential to become the next generation of high-speed rail transport due to its passive stabilization and virtually no magnetic resistance. From the maglev dynamics views, the damping between the levitated superconductor and the permanent magnet will play an important role to the further vehicle bogie design. The early experiments on HTS maglev damping illustrates that the data was very small in the no-load conditions and lacks the significant exploration of the practical-employed three-seed YBCO bulk as the levitator material. In addition, the empirical expression of the damping coefficient and the working height is still unsolved for applications. Focusing on the vertical damping of the HTS levitator levitated above the practical Halbach magnet track, a vertical vibration damping test bench is designed to conduct experiments in free levitation. Firstly, the effects of three main working factors like load, field cooling height (FCH) and excitation strength, on the vertical damping of the HTS levitation are investigated under different experimental loads. It is interesting to find the HTS levitation shows strong damping behaviors during the practical load operations above the magnet track. Based on the experimental data and theoretical analysis, the vertical damping of the HTS Maglev engineering vehicle is derived as 2×104 Ns/m, which can be close to that of a superconducting electrodynamic levitation vehicle. Secondly, the empirical formula of damping-working height is established by combining the experimental data with the theoretical formula model. It is found that the excitation strength affects the decay of damping but has little effect on the damping magnitude. Furthermore, the phenomenon of keeping constant damping ratio at the same FCH is found even though the other conditions change. This paper show evidences that the HTS maglev system is not a weakly damped system and has a strong nonlinearity in the vertical damping. The proposed empirical formula can provide reference for the bogie design of HTS maglev train.