This study deals with the magnetically levitated capsule train running through the sub-vacuum. Due to the low air resistance and friction between capsule and tube, the capsule train can theoretically reach over 1,000km/h speed. As levitation, the superconducting electrodynamic suspension(EDS) technique is used in the capsule train. Since EDS levitation inherently has very small electromagnetic damping and non-linear magnetic stiffness, the vibration caused from outer disturbance such as guideway irregularity should be carefully investigated and then reduced by using additional devices for ride comfort improvement. In this study, firstly the capsule train model is introduced and the dynamic analysis including non-linear magnetic stiffness is conducted. Then, as ride comfort improvement method, the semi-active suspension between carbody and bogie is applied and the effectiveness is examined. Lastly, through the hardware-in-the-loop simulation(HILS) system composed with the capsule train dynamic model and the real actuator as semi-active suspension, performances is experimentally examined.