Abstract A rotating flexible annular micro-disk under thermoelastic coupling is modeled to investigate the thermoelastic damping in the rotating micro-disk in Microdrives. Transverse deflection of the micro-disk is considered as a function of both disk radial and circumferential coordinates, and its thermoelastic temperature increment is modeled by simultaneously involving disk thickness, radial and circumferential coordinates. Heat convection boundaries are assumed at disk top and bottom surfaces. System governing equations with the centrifugal stresses of disk rotation and thermoelastic coupling terms are discretized along disk radial direction by an annular finite element, and a quadratic eigenvalue problem is yielded to determine the thermoelastic damping. Mode shapes of the transverse deflection and temperature increment are presented, effects of disk rotation, surface convection and ambient temperature on natural frequency, frequency shift and thermoelastic damping are investigated. The maximum thermoelastic damping is obtained by optimizing disk thickness, inner radius and radial width.