Surface reconstruction and phase transformation in nanomaterials can result in a significant rise in temperature due to the release of stored energy called "latent heat." To simulate this behavior, we propose a hybrid continuum partial differential equation for non-Fourier heat transfer with a stochastic source term modeled using a kinetic Monte Carlo (KMC) algorithm for time-dependent rates to account for the latent heat release as the temperature is changing. The parameters required for the method are obtained through independent atomistic calculations. This includes energy barriers for KMC rates obtained using nudged elastic band calculations, and the non-Fourier thermal parameters obtained using a novel thermal parameter identification scheme described in this paper. As a demonstration of the approach, we study the superheating of silicon nanobeams observed in non-equilibrium molecular dynamics (NEMD) simulations. In these simulations, silicon (001) surfaces undergo a reconstruction from the ideal diamond crystalline surface to a reconstructed structure involving the formation of rows of dimers along a (110) direction. This reconstruction is accompanied by latent heat release that causes the nanobeam to dramatically superheat. The evolution of the nonuniform temperature profile along the nanobeam predicted by the continuum-KMC method is in excellent agreement with the NEMD results. A logarithmic dependence of the superheating temperature on nanobeam length is observed and theoretically discussed. (C) 2016 Published by Elsevier Ltd.