Using micromagnetic simulation, we investigated the effect of thickness of a nanodisk on a resonance frequency of vortex gyration. We observed that the resonance frequency increases with increasing thickness in both cases of 2-dimensional (2D) and 3-dimensional (3D) calculation. However, there is a difference in the increasing rate of resonance frequency between 2D and 3D modeling owing to dynamically developed inhomogeneous magnetic texture along the thickness direction of disk in 3D modeling.