In the present paper, an isogeometric analysis formulation along with the Nitsche technique is implemented based on the first order shear deformation plate theory to investigate the aero-thermo-elastic panel flutter behavior of a functionally graded (FG) plate containing cracks in the supersonic flow field. A FG material is considered with temperature-dependent mechanical properties distributed in the plate thickness according to the power law. The temperature distribution in the plate thickness is calculated through solution of the one-dimensional steady-state conductive heat transfer equation while the surface temperatures are kept fixed. The physical contact and the crack growth phenomena are overlooked in the present research. The panel flutter behavior is investigated under combination of crack orientation, crack length, thermal conditions, flow direction, FG volume fraction index and boundary conditions. The accuracy and quality of the present isogeometric formulation is shown in comparison with those available in literature.