Abstract: There are complex microstructures of functionally graded materials, and their internal structures are more complex than those of homogeneous materials. Therefore, the analytic solution of the functionally graded structure is difficult to obtain. A new microelement method for the analysis of functionally graded structures was suggested to establish the quantitative relation between the macro-character and microstructures of functionally graded materials, and the mechanism, that different combination and variation of materials have different macro-characters, can be found. The dynamic analyses of functionally graded structures with gap, impurities and component mutation are performed by the microelement method, and the three-dimensional values of natural frequency and the three-dimensional distributions of the mode shape are given in this paper, and there are great influences of the gaps, impurities and component mutation on the macro dynamic characters of the functionally graded structures.