Pump annular seals can cause fluid reaction forces that have great effects on the vibration characteristic and stability of a pump system. For this reason, it is important to study rotordynamic characteristics of annular seals. In this paper, a new transient computational fluid dynamics (CFD) method with dynamic mesh is proposed to investigate rotordynamic characteristics of the pump annular seal. The reliability of the transient CFD method is validated by comparison with the results from the experiment and the bulk-flow method, and the relationship between the seal length and rotordynamic characteristics is investigated by the transient CFD method. The results indicate that direct stiffness decreases sharply even turns to negative as the seal length increases, this phenomenon may change the direction of fluid force on the rotor surface and affect supporting condition of the pump rotor. With the increasing seal length, the whirl frequency ratio gradually increases, which would weaken the stability of the pump rotor system.