Application of the isogeometric method is illustrated for free and forced vibration analyzes of sinusoidally corrugated functionally graded carbon nanotube reinforced composite (FG-CNTRC) thin panels. These panels can be used as a potential structure for morphing skin applications. The nanocomposite panel is fabricated from a polymeric matrix which is reinforced by carbon nanotubes (CNTs). The volume fraction of CNTs varies based on the four models of functionally graded (FG). The Kirchhoff-Love (KL) shell theory is employed to model the kinematic behavior of sinusoidally corrugated panels (SCPs) with a variable radius of curvature. The multiple patches approach is approved to model the structure. In this model, the bending strip method (BSM) is applied at the intersection of the patches. The temporal response of the panel under different transverse dynamical loadings is predicted via the Newmark time-marching scheme. A detailed comparison study is performed to demonstrate the validity and efficiency of the proposed isogeometric analysis (IGA). The numerical results demonstrate that the computationally effective IGA can provide accurate results due to the capability of precisely approximating any segments of the corrugation. Furthermore, the effects of different configurations of CNTs and various geometrical parameters such as corrugation amplitude, number of corrugation units and panel aspect ratio are presented on the natural frequency and dynamic response of the sinusoidally corrugated FG-CNTRC panels.