AlGaN/GaN heterojunction-based high-electron-mobility transistors (HEMTs) have significant advantages of high carrier concentration, high electron mobility, and large breakdown voltage, and show promising potential as power devices. Being widely used in semiconductor manufacturing, dry etching process is capable of fabricating microstructures and thinning substrate from backside, which is good for developing flexible devices. Here, we investigate the effect of backside dry etching of Si substrate on the physical and electrical properties of AlGaN/GaN HEMTs. The physical properties were characterized by scanning electron microscope, Raman spectra, and x-ray diffraction (XRD). After the dry etching process, the peak red-shift of GaNE2mode indicates an increase of tensile stress, and the XRD rocking curve of GaN film shows to a certain extent decreased dislocation density. Furthermore, the maximum saturation current density and maximum transconductance of the HEMTs are improved by 21.1% and 25.5%, respectively. The approach of backside dry etching for thinning Si substrate would contribute to the optimization of GaN heterojunction-based devices, and also provide inspirations for the development of flexible and robust power devices.