To overcome the overstiffness and imprecise magnetoelectroelastic coupling effects of finite element method (FEM), we present an inhomogeneous cell-based smoothed FEM (ICS-FEM) of functionally graded magnetoelectroelastic (FGMEE) structures. Then the ICS-FEM formulations for free vibration calculation of FGMEE structures were deduced. In FGMEE structures, the true parameters at the Gaussian integration point were adopted directly to replace the homogenization in an element. The ICS-FEM provides a continuous system with a close-to-exact stiffness, which could be automatically and more easily generated for complicated domains, thus significantly decreasing the numerical error. To verify the accuracy and trustworthiness of ICS-FEM, we investigated several numerical examples and found that ICS-FEM simulated more accurately than the standard FEM. Also the effects of various equivalent stiffness matrices and the gradient function on the inherent frequency of FGMEE beams were studied.