The free vibration of a spinning flexible disk-spindle system supported by hydro dynamic bearings (HDB) in an HDD is analyzed by FEM. The spinning flexible disk is described using Kirchhoff plate theory and von Karman non-linear strain, and its rigid body motion is also considered. It is discretized by annular sector element. The rotating spindle which includes the clamp, hub, permanent magnet and yoke, is modeled by Timoshenko beam including the gyroscopic effect. The flexible supporting structure with a complex shape which includes stator core, housing, base plate, sleeve and thrust pad is modeled by using a 4-node tetrahedron element with rotational degrees of freedom to satisfy the geometric compatibility. The dynamic coefficients of HDB are calculated from the HDB analysis program, which solves the perturbed Reynolds equation using FEM. Introducing the virtual nodes and the rigid link constraints defined in the center of HDB, beam elements of the shaft are connected to the solid elements of the sleeve and thrust pad through the spring and damper element. The global matrix equation obtained by assembling the finite element equations of each substructure is transformed to the state-space matrix-vector equation, and the associated eigen value problem is solved by using the restarted Arnoldi iteration method. The validity of this research is verified by comparing the numerical results of the natural frequencies with the experimental ones. Also the effect of supporting structures to the natural modes of the total HDD system is rigorously analyzed.