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The performance damage mechanism of InP-based high electron mobility transistors (HEMTs) after proton irradiation has been investigated comprehensively through induced defects. The effects of the defect type, defect energy level with respect to conduction band ET, and defect concentration on the transfer and output characteristics of the device are discussed based on hydrodynamic model and Shockley–Read–Hall recombination model. The results indicate that only acceptor-like defects have a significant influence on device operation. Meanwhile, as defect energy level ET shifts away from conduction band, the drain current decreases gradually and finally reaches a saturation value with ET above 0.5 eV. This can be attributed to the fact that at sufficient deep level, acceptor-type defects could not be ionized any more. Additionally, the drain current and transconductance degrade more severely with larger acceptor concentration. These changes of the electrical characteristics with proton radiation could be accounted for by the electron density reduction in the channel region from induced acceptor-like defects.