Aiming at the seal fluid excitation problem caused by rotor eccentricity, a new eccentricity self-adjusting seal structure which can decrease rotor eccentricity was designed and its vibration suppression mechanism was explored. Theory concludes that the vibration suppression effect is the best only when the designed structure natural frequency is consistent with the rotor-seal exciting frequency. Otherwise, the effect becomes weaker. With using water as the sealing media, the designed structure natural frequencies under different spring stiffness were measured specifically. With changing rotating frequency, the structure vibration suppression laws were experimentally researched. Results show that the structure frequencies increase with the increased spring stiffness but are much higher than the rotor-seal exciting frequency. The vibration amplitude decrease ratios are not notable and only maintain between 10%~20%. Then the eccentricity structure was put in the water and its frequency in water was measured. Similarly, its vibration suppression laws in water were experimentally researched. Results demonstrate that the structure in water frequencies still increase with the increased spring stiffness but are lower about 40% than in the air. So structure frequencies in the water are closer to the exciting frequency and the vibration suppression effects in this condition are more obvious. Finally, the maximum vibration amplitude decrease ratio reaches to 41.27%.