<p>Energy dissipation and frequency shift (FS) due to the thermoelastic coupling (TEC) restrict the improvement of resonator quality factor (Q-factor). However, the mechanisms in functionally graded materials (FGMs) micro-resonators are unclear because of the complex nonlinear TEC equations and scale-dependent effect. This paper presents a TEC model for FGMs circular plates based on the surface elasticity theory (SE theory) and the nonlocal dual-phase-lagging heat conduction model (NDPL model). The layered homogenization method is used to solve the nonlinear heat conduction equation arising from the variation of material components along the plate’s thickness in a power-series form. An analytical solution for the resonant frequency is obtained by exploiting the similarity between the nonlinear TEC vibration equation of FGMs circular plates and that of homogeneous circular plates under adiabatic conditions. The analytical solutions for thermoelastic damping (TED) and FS of FGMs circular plates are derived. The reliability of the layered homogenization method is verified by numerical result stability. Numerical results show that the functional gradient index and scale-dependent effect such as nonlocal thermal parameter significantly influence the TEC behavior of FGMs circular plates. When considering the scale-dependent effect, the reduction amplitudes of TED, FS, and frequency attenuation (FA) of the FGMs plate are lower than those of the full N₃Si₄ plate and the full Ni plate, namely, compared with isotropic homogeneous circular plates, FGMs circular plates have a lower FS amplitude and better thermal dissipation adjustability, thus offering higher operating accuracy. These findings are crucial for improving micro-resonator design accuracy.</p>