Recently, the hard disk drive (HDD) industry has tried to use a compatible spindle system regardless of the number of disks because of the resulting cost reduction and standardization of components. The center of gravity (CG) location predominantly affects the disk and slider off-track vibration, which is why the rocking mode of a spindle system is affected by the CG. Any changes to the CG affect the operational vibration of the spindle system. In a compatible fluid dynamic bearing (FDB) spindle system, changing the number of disks may alter the CG. Nevertheless, research into the compatibility of FDB designs has not been undertaken. In this study, FDB design parameters were selected to reduce the slider off-track vibration with variations in the CG considering a compatible spindle system. First, a verified finite element (FE) model of a spindle system was constructed. The amplitude and frequency of the rocking mode were compared between a one-disk spindle system and a two-disk spindle system using the FE model, considering the relationship between the CG location, which is changed by the number of disks, and the location of the upper and lower journal bearings. HDD prototypes were then manufactured using the improved design. Based on the manufactured spindle system, the variations in the rocking mode characteristics and slider off-track vibration were measured and operational vibration tests were performed to verify the effect of the number of disks on the slider off-track vibration. An improved FDB spindle design was developed with a reduced rocking mode, and a compatible spindle system was proposed.