Free vibration of coupled system including clamped-free thin circular plate with hole submerged in three-dimensional cylindrical container filled with inviscid, irrotational and compressible fluid is investigated in this work. Numerical approach based on the finite element method (FEM) is performed using the Comsol Multiphysics software, in order to analyze qualitatively the vibration characteristics of the plate. Plate modeling is based on Kirchhoff–Love plate theory. Velocity potential is deployed to describe the fluid motion since the small oscillations induced by the plate vibration is considered. Bernoulli’s equation together with potential theory is applied to get the fluid pressure on the free surface of the plate. To prove the reliability of the present numerical solution, a comparison is made with the results in the literature, which shows a very good agreement. Then, different parameters effect including fluid density, fluid height, free surface wave, hole radius and hole eccentricity on the natural frequencies of the coupled system is discussed in detail. Some three-dimensional mode shapes of the submerged plate are illustrated. Furthermore, the obtained results can serve as benchmark solutions for the vibration control, parameter identification and damage detection of plate.