In this study rectangular AlGaN/AlN/GaN heterostructure field-effect transistors (HFETs) with 22-nm and 12-nm AlGaN barrier layers are fabricated, respectively. Using the measured capacitance–voltage and current–voltage characteristics of the prepared devices with different Schottky areas, it is found that after processing the device, the polarization Coulomb field (PCF) scattering is induced and has an important influence on the two-dimensional electron gas electron mobility. Moreover, the influence of PCF scattering on the electron mobility is enhanced by reducing the AlGaN barrier thickness. This leads to the quite different variation of the electron mobility with gate bias when compared with the AlGaN barrier thickness. This mainly happens because the thinner AlGaN barrier layer suffers from a much stronger electrical field when applying a gate bias, which gives rise to a stronger converse piezoelectric effect.