Rotor dynamics and flow characteristics are computed for a honeycomb seal and a corresponding labyrinth seal. Firstly, rotor dynamic parameters, such as amplitude and frequency of vibration are calculated. Then these parameters are used for unsteady fluid flow computation. Numerical results indicate that the rotor vibration can reduce sealing performance and result in additional aerodynamic force on rotor. Further, the aerodynamic forces tend to reduce the self-excited vibration of rotor, and this effect becomes more apparent with the increase of pressure difference. Vortex in seal cavities is deemed to be the primary cause of the above mentioned results. The differences between the two types of seals are presented in this article. Finally, authors conclude that suitable structure design of honeycomb and labyrinth seals, or their combination can minimize rotor vibration.