Due to its excellent thermal protection effect, crushed rock are widely used in embankment engineering in permafrost regions. Accurately describing the heat transfer mechanism on the surface of crushed rock plays an important role in predicting the long-term service performance of crushed rock embankments. This article takes the crushed rock slope protection of the Qinghai Tibet Railway as the research object, and based on the surface energy balance equation, studies the local thermal non-equilibrium (LTNE) heat transfer mechanism reflecting the thermal boundary of the crushed rock skeleton under the interaction of radiation, convection, and conduction on the surface of the crushed rock layer, and develops a new calculation method for the thermal boundary. Through experiments and theoretical calculations on different embankment slope orientations, it was found that there is indeed a LTNE phenomenon on the surface of crushed rock due to differences in the properties of pore fluids and crushed rock skeletons. The use of a new thermal boundary calculation method can better describe the LTNE boundary of the crushed rock layer surface. This boundary model is helpful for further exploring the temperature changes and non-equilibrium effects of crushed rock slopes on the Qinghai Tibet Plateau under different external influencing factors such as wind speed, albedo, roughness, and climate warming. In addition, research on the temperature rise induced boundary warming of embankment stone slope protection under different warming scenarios has found that under the influence of climate warming, the boundary warming of stone blocks exhibits nonlinear characteristics and lags behind the change pattern of temperature rise.