High-temperature processing steps are frequently used in manufacture of AlGaN/(AlN/)GaN high electron mobility transistors (HEMTs). The thermal budgets drive Al diffusion into the GaN channel, increase alloy disorder scattering (ADS) of the two-dimensional-electron-gas (2DEG), and degrade the 2DEG mobility. By correlating the ADS to device thermal budget, we propose an analytical model to calculate the ADS limited mobility as a function of Al diffusion lengths (LD,Al) in AlGaN/(AlN/)GaN HEMTs. The simulation indicates that the ADS is a significant mobility degradation mechanism whose scattering rate increases with the 2DEG density and the LD,Al. The findings explain the generally observed trends in the literature that the 2DEG mobility and sheet resistances of GaN heterostructures degrade with increased thermal budgets, especially after >900 °C processing.