In this study, a free vibration model of bi-directional functionally graded (BD-FG) annular microplates is established based on the modified couple stress theory (MCST) and the first-order shear deformation theory (FSDT), and the corresponding governing equations are derived from Hamilton’s principle. The annular microplates are assumed to be composed of metal and ceramic materials, and the equivalent material properties are a combination of power-law function and exponential ones. The generalized differential quadrature method (GDQM) is used to obtain the vibration frequencies and mode displacements for the C–C, S–C, C–S, and S–S (S: simply supported; C: clamped) annular microplates. The convergence and validity of the proposed model are verified through selective numerical examples. Further, the effects of gradient index, material length scale parameter, boundary conditions, and geometrical dimensions on the symmetric/asymmetric vibration frequencies of the annular microplate are explored. The modal assurance criterion is applied to estimate the influence of the radial gradient index and material length scale parameter on different-order mode displacements of the annular microplate. The results show that: (1) the vibration frequencies of the annular microplate are sensitive to changes in the geometry and boundary conditions; (2) compared with the axial gradient index, the radial gradient index not only affects the vibration frequencies of the annular microplate, but also impacts the distribution of the highest and lowest points of the vibration mode displacements as well as the vibration mode nodal lines; (3) as the material length scale parameter increases, the vibration frequencies are significantly increased, and the higher-order vibration modes of the annular microplate also change.