The statistical photoelectric properties of InGaN/GaN MQWs solar cells under proton irradiation were studied. Three groups of devices were irradiated with 3 MeV proton beams with fluences of 1.0 × 1011 cm−2, 5.0 × 1011 cm−2, and 1.0 × 1012 cm−2. Averaged experiment results showed that the open circuit voltage (VOC) and fill factor (FF) always decreased. In contrast, the short circuit current density (JSC) and photoelectric conversion efficiency (η) increased first and then decreased with the increase of fluence. Firstly, the donor-like defects of InGaN layer in active region played a major role in increasing JSC and η when the fluence was relatively low. Due to the introduction of donor-like defects, extra free electrons were produced, which lead to an increase in the number of effective carriers. With the further increasing of proton fluence, the number of free electrons caused by donor-like defects in the used InGaN material (low indium component) increased slowly due to pinning effect. However, additional point defects (Ga vacancies) increased significantly. Ga vacancies can act as effective non-radiative recombination centers, thereby reducing the number of effective carriers. The combined effect of pinning effect and non-radiative recombination process is responsible for the first increase and subsequent decline of JSC and η.