Exact assessment of self-heating is of great importance to the thermal management of electronic devices, especially when completely considering the cross-scale heat conduction process. The existing simulation methods are either based on convectional Fourier's law or limited to small system sizes, making it difficult to deal with noncontinuum thermal transport efficiently. In this paper, a hybrid phonon Monte Carlo diffusion method is adopted to predict device temperature in ballistic–diffusive regime. Heat conduction around the heat generation region and boundaries are simulated by phonon Monte Carlo (MC) method, while the other domain is by Fourier's law. The temperature of the hybrid method is higher than that of Fourier's law owing to phonon ballistic transport, and the calculation efficiency of the hybrid method is remarkably improved compared with phonon MC simulation. Furthermore, the simulation results indicate that the way of modeling self-heating has a remarkable impact on phonon transport. The junction temperature of the heat source (HS) scheme can be larger than that of the heat flux (HF) scheme, which is opposite to the result under Fourier's law. In the HS scheme, the enhanced phonon-boundary scattering counteracts the broadening of the heat source, leading to a stronger ballistic effect and higher temperatures. The conclusion is verified by a one-dimensional analytical model. This work has opened up an opportunity for the fast and extensive thermal simulations of cross-scale heat transfer in electronic devices and highlighted the influence of heating schemes.