Undoped GaN-based metal-oxide-semiconductor high-electron-mobility transistors (MOS-HEMTs) with atomic-layer-deposited Al2O3 gate dielectrics are fabricated with gate lengths from 1 up to 40 μm. Using a two-dimensional numerical simulator, we report the results of self-heating simulations of the GaN-based MOS-HEMTs, including hot electron and quantum effects. The simulated electrical characteristics are in good agreement with reported experimental data. The effect of the gate and source/drain extension lengths on both the output performance and self-heating is discussed in detail, allowing for device optimization. The dissipated Joule electric power causes the self-heating effects, which lead to negative differential output conductance. Our results demonstrate that the hot electrons make a negligible contribution to the negative differential output conductance in our long channel MOS-HEMTs. In order to investigate their joint interactions to the MOS-HEMT’s operation, the different static interface trap and charge densities created at the AlGaN/Al2O3 interface are considered in the output characteristics. Results show that the presence of the interface charges and traps are directly responsible for the observed current collapse and device switching in the GaN-based MOS-HEMTs. The self-heating is also strongly affected due to the fluctuation of the interface states.