A high quality factor (Qfactor) is a critical parameter determining the sensing sensitivity and frequency stability of MEMS resonators. However, given the complex energy dissipation mechanisms at the micro/nanoscale, conventional design approaches relying on geometric intuition struggle to maximize the Qfactor within an environment of multiple coupled damping sources. To address this challenge, this paper proposes a topology optimization design methodology tailored for highQ MEMS beam resonators. First, grounded in thermoelasticity and elastic wave radiation theories, a comprehensive multiphysics simulation framework incorporating both thermoelastic damping (TED) and anchor loss is established. By integrating Perfectly Matched Layers (PMLs) with coupled thermalstructural equations, the total energy dissipation of the resonator is quantified with high precision. Subsequently, a densitybased topology optimization algorithm is employed to evolve the structure of a silicon clampedclamped beam, with the objective of maximizing the Qfactor of the fundamental mode. The study yields two novel topological configurations exhibiting significantly reduced energy loss. Physical mechanism analysis reveals that the optimized material distribution effectively interrupts transverse heatflow pathways, thereby suppressing TED, while simultaneously inducing a “softclamping” redistribution of strain energy near the anchors to minimize energy leakage into the substrate. Simulation results demonstrate that, compared with a conventional solid straight beam of identical dimensions, the optimized designs achieve an approximately sixfold enhancement in the overall Qfactor. This work confirms the effectiveness of the multiphysicscoupled topology optimization strategy, providing new theoretical guidance and technical pathways for the design of highperformance MEMS resonators.