An enhanced InGaN/GaN multiple-quantum-wells (MQWs) solar cell was exposed to 3 MeV protons. The performance of the solar cell, including the current-voltage characteristics and external quantum efficiency (EQE), degraded after irradiation with 3 MeV protons. The ideality factor became higher with increased proton fluence, which indicates defects were introduced into the device. The decreased peak intensity and increased full width at half maximum (FWHM) in photoluminescence (PL) spectra from InGaN, and the increased FWHM values of the InGaN satellite peaks from (002) ω-2θ diffraction curves all indicate the active region degraded. Moreover, according to the correlation between the ideality factor, the negative of one-thousandth of InGaN peak intensity, and FWHM of the PL spectra in the active region, we deduced that defects were introduced in the active region. Furthermore, we deduced the defects are Ga vacancies using SRIM software simulation. The enhanced yellow band may be affected by Ga vacancies since the other influencing factors in our experiment could be excluded. Based on the above analysis, we infer that Ga vacancies may be introduced in the active region after irradiation with 3 MeV proton, which may lead to degraded electrical parameters in InGaN/GaN MQWs solar cells.