This paper presents a finite element method to analyze the free vibration of a flexible HDD composed of the spinning disk-spindle system with fluid dynamic bearings(FDBs), the head-suspension-actuator with pivot bearings, and the base plate with complicated geometry. Experimental modal testing shows that the proposed method well predicts the vibration characteristics of a HDD. This research also shows that even the vibration motion of the spinning disk corresponding to half-speed whirl and the pure disk mode are transferred to a head-suspension-actuator and base plate through the air bearing and the pivot bearing consecutively. The proposed method can be effectively extended to investigate the forced vibration of a HDD and to design a robust HDD against shock.