Effects of partition wall type, partition wall number and cavity depth on the leakage and rotordynamic characteristics of the pocket damper seal (PDS) were numerically investigated using a presented 3D transient computational fluid dynamics (CFD) method based on the multifrequency elliptical whirling orbit model. The accuracy and availability of this transient CFD method and the multifrequency elliptical whirling orbit model were demonstrated with the experimental data of the experimental eight-bladed fully partitioned pocket damper seal (FPDS). The leakage flow rates and frequency-dependent rotordynamic coefficients of PDS were computed for two types of partition wall (namely conventional PDS and fully partitioned PDS), four partition wall numbers including the labyrinth seal (no partition wall) and six cavity depths including the plain smooth seal (zero cavity depth) at operational conditions with or without inlet preswirl and 15,000 rpm rotational speed. The numerical results show that the FPDS has the similar leakage performance and more superior stability capacity than the conventional PDS. The FPDS possesses slightly larger leakage flow rate (∼2.6–4.0% larger) compared to the labyrinth seal. Eight is a preferable value for the partition wall number to gain the best leakage performance of the FPDS with the least manufacturing cost. The FPDS possesses significantly larger stiffness and damping than the labyrinth seal. Increasing partition wall number results in a significant increase in the direct stiffness but limited desirable effect on the effective damping. The FPDS possesses the lowest leakage flow rate when the cavity depth is about 2.0 mm. Compared to the plain smooth seal, the FPDS possesses larger positive direct stiffness and significantly less direct damping and effective damping. Increasing cavity depth results in a significant decrease in the stabilizing direct damping and the magnitude of the destabilizing cross-coupling stiffness. 3.175 mm is a preferable value of the cavity depth for which the effective damping of the FPDS is largest, especially for the concerned frequencies (80–120 Hz) where most multistage high-pressure centrifugal compressors have stability problem.