The problems of functionally graded materials are supposed to be studied incorporating their microstructures. The microelement method proposed here is characterized by this capability. In this work, by using the Fortran source program of microelement method established on the basis of existing finite element method, 3-D dynamic analysis of functionally graded material plates with different openings is performed. It can be known from the numerical results that the shapes and number of openings have a significant influence on natural frequency and basic vibration modes of functionally graded material plates, which is different from the results of homogeneous plates. These results are significant to applications of functionally graded material plates with openings.