We studied how substrate thinning affected the electronic transport characteristics of AlGaN/GaN HEMTs. By thinning their sapphire substrate from 460 mu m to 80 mu m, we varied the residual stress in these HEMTs. The thinned sample showed decreased drain-source current and occurrence of kink effect. Furthermore, shown by current transient measurements and time constant analysis, the detrapping behaviors of trap states shifted toward a larger time constant, and the detrapping behavior under the gate and in the gate-drain access region showed increased amplitude. By using pulsed current-voltage measurements, the thinned sample showed a positive shift of the threshold voltage, a decrease in peak transconductance, and an aggravation in current collapse, as compared with the thick one. The degradation of electrical behavior were associated with the structural degradation, as confirmed by the increase of pit density on the thinned sample surface.