In this paper, the effects of different cavitation bubble on the natural frequency, mode shape and hydrodynamic damping of the NACA0009 hydrofoil are investigated by numerical simulation method. The cantilever truncated hydrofoil model is set in a high-speed water tunnel. The dynamic characteristics of the hydrofoil structure is affected by the fluid-structure coupling. Compared to the properties of water, the density of cavitation bubbles decreases, causing an increase in the natural frequency of the structure, and the decrease in the speed of sound also causes a change in the mode shape. The growth rate of frequency under unit chord length cavitation is nonlinear as the cavitation bubble length increases. By defining a modal displacement function to compare the structural mode shapes, cavitation intensifies the bending and torsional deformation of the hydrofoil. Even if the volume of cavitation bubbles is small, the inhomogeneous distribution of acoustic pressure and changes in cavitation bubble properties can cause changes in the structural mode shapes. The one-way FSI numerical method for hydrodynamic damping in cavitating flow is established and the applicability of this method is verified by the calculation of damping in water. For the first bending mode fc1, the hydrodynamic damping with 50% chord length (0.5lc) stably attaching cavitation is simulated. As the length of the cavitation bubble increases to 0.8lc, the damping value becomes smaller. The research in this paper lays the foundation for analysing the dynamic characteristics of hydraulic machinery with cavitation using numerical simulation method.