Degradation on DC characteristics of AlGaN/GaN high electron mobility transistors (HEMTs) after applying pulsed gate stress at cryogenic temperatures is presented in this paper. The nitrogen vacancy near to the AlGaN/GaN interface leads to threshold voltage of stress-free sample shifting positively at low temperature. The anomalous behavior of threshold voltage variation (decrease first and then increase) under gate stressing as compared to stress-free sample is observed when lowing temperature. This can be correlated with the pre-existing electron traps in SiNX layer or at SiNX/AlGaN interface which can be de-activated and the captured electrons inject back to channel with lowering temperature, which counterbalances the influence of nitrogen vacancy on threshold voltage shift.