In this article, based on high-order sandwich panel theory and modified strain gradient theory, free vibration analysis of a micro-magneto-electro-elastic sandwich panel with a transversely flexible core and functionally graded carbon nanotube–reinforced nanocomposite face sheets is investigated. Also, the influences of temperature-dependent material properties and various circuit boundary conditions such as open and closed are considered in this study. Carbon nanotubes are arranged in longitudinal direction inside polyvinylidene fluoride matrix with various functionally graded (FG) distributions such as uniform, FG-V, FG-A, FG-X, and FG-O in the face sheets. The generalized rule of mixture is employed to predict mechanical, electrical, magnetic, and thermal properties of micro-sandwich composite panel. The classical shell theory and an elasticity high-order theory are used for the face sheets and the core, respectively. Then, the governing equations of motion are derived using Hamilton’s principle. In this article, the influences of the volume fraction, the various distributions of carbon nanotubes, the multi-physical fields, open- and closed-circuit boundary conditions, the material length scale parameters, different face sheet and core thicknesses, and temperature changes on the natural frequency are investigated, and the obtained results show that these influences play an important role in the natural frequencies and can be used in order to prevent the resonance phenomenon and also for manufacturing process design and optimization of micro-magneto-electro-elastic composite sandwich cylindrical panels.