Thermoelastic damping has emerged as a critical issue in the modeling and design of micro and nanomechanical systems. Therefore, an extensive research interest is being devoted towards the reduction in thermoelastic damping for micro and nanomechanical systems. The present study intends to examine thermoelastic damping in nanobeam resonators using the modified couple stress theory and Eringen’s nonlocal elasticity theory, thus so-called modified nonlocal couple stress theory within the context of the recently proposed Moore–Gibson–Thompson thermoelasticity theory. In order to observe size effects, the size-dependent coupled thermoelastic equations are derived by combining modified couple stress theory and nonlocal elasticity theory in the frame of Moore–Gibson–Thompson thermoelasticity. The coupled governing equations for thermoelastic damping of nanobeam resonators are solved analytically in terms of the inverse quality factor. The size-dependent thermoelastic damping of nanobeams is presented graphically with the help of numerical results predicted by modified nonlocal couple stress theory. The results obtained under the combined effects of modified couple stress theory and nonlocal theory in the present context are further compared to those of the classical, modified couple stress, and nonlocal elasticity theories as special cases of the modified nonlocal couple stress theory. It is observed that thermoelastic damping weakens at the submicron scale under Eringen’s nonlocal elasticity theory, whereas it becomes greater at the submicron scale under modified couple stress theory. However, at the submicron scale, the modeling of nanobeam resonators using modified nonlocal couple stress theory reveals a smaller amount of thermoelastic damping than modified couple stress, nonlocal, and classical theories. In addition, as compared to the Green–Naghdi thermoelasticity theory of type III (GN-III), the Moore–Gibson–Thompson model predicts a higher thermoelastic damping value, while agreeing with the results predicted by the Lord–Shulman (LS) model under modified nonlocal couple stress theory. Some important points highlighted here are believed to be useful in the design of mechanical resonators at micron and submicron scales.