The damage mechanism of proton irradiation in InP/InGaAs heterostructures was studied. The deep level traps were investigated in detail by deep level transient spectroscopy (DLTS), capacitance–voltage (C–V) measurements and SRIM (the stopping and range of ions in matter, Monte Carlo code) simulation for non-irradiated and 3 MeV proton-irradiated samples at a fluence of 5 × 1012 p/cm2. Compared with non-irradiated samples, a new electron trap at EC-0.37 eV was measured by DLTS in post-irradiated samples and was found to be closer to the center of the forbidden band. The trap concentration in bulk, the interface trap charge density and the electron capture cross-section were 4 × 1015 cm−3, 1.8 × 1012 cm−2, and 9.61 × 10−15 cm2, respectively. The deep level trap, acting as a recombination center, resulted in a large recombination current at a lower forward bias and made the forward current increase in InP/InGaAs heterostructures for post-irradiated samples. When the deep level trap parameters were added into the technology computer-aided design (TCAD) simulation tool, the simulation results matched the current–voltage measurements data well, which verifies the validity of the damage mechanism of proton irradiation.