Thermal frequency of the graded nanotube-reinforced composite structure embedded with shape memory alloy (SMA) fiber has been computed first time numerically using a micromechanical multiscale finite element material model (In house computer code). The smart nanotube-reinforced composite structure has been formulated through the higher-order kinematics including the shear deformations. The governing equation of the structure has been obtained via Hamilton's principle considering the temperature effect and the temperature-dependent properties. After the necessary verification of the derived model, a set of numerical examples are solved which indicates a substantial improvement in structural stiffness due to the presence of SMA.