Due to nonlocal and strain gradient effects with rigid and deformable boundary conditions, the thermal vibration behavior of perforated nanobeams resting on a Winkler elastic foundation (WEF) is examined in this paper. The Stokes transformation and Fourier series have been used to achieve this goal and to determine the thermal vibration behavior under various boundary conditions, including deformable and non-deformable ones. The perforated nanobeams’ boundary conditions are considered deformable, and the nonlocal strain gradient theory accounts for the size dependency. The problem is modeled as an eigenvalue problem. The effect of parameters such as the number of holes, elastic foundation, nonlocal and strain gradient, deformable boundaries and size on the solution is considered. The effects of various parameters, such as the length of the perforated beam, number of holes, filling ratio, thermal effect parameter, small-scale parameters and foundation parameter, on the thermal vibration behavior of the perforated nanobeam, are then illustrated using a set of numerical examples. As a result of the analysis, it was determined that the vibration frequency of the nanobeam was most affected by the changes in the dimensionless WEF parameter in the first mode and the changes in the internal length parameter when all modes were considered.