AlGaN/GaN high-electron-mobility transistors (HEMTs) with two different gate–drain distances (30 μm and 10 μm) were exposed to 1 MeV, 0.6 MeV, and 0.4 MeV protons at a fluence of 2.16 × 1012 cm−2. The gate–channel electron density and low-field mobility were obtained by measuring the capacitance–voltage characteristics and current–voltage characteristics. After proton irradiation, the gate–channel low-field electron mobility of the AlGaN/GaN HEMT with a 30 μm gate–drain distance increases and that with a 10 μm gate–drain distance decreases. It is studied and found that the mobility behavior is related to the polarization Coulomb field scattering, and the proton irradiation influences the intensity of the polarization Coulomb field scattering by changing the polarization/strain distribution in the barrier layer. The different gate–drain distances correspond to different variation trends of scattering intensity. The effect of 1 MeV protons on the barrier layer is smaller compared with 0.6 MeV and 0.4 MeV protons, so the mobility variation is smaller.