The effects of proton irradiation on CMOS Single-Photon Avalanche Diodes (SPADs) are investigated in this article. The I–V characteristics, dark count rate (DCR), and photon detection probability (PDP) of the CMOS SPADs were measured under 30 MeV and 52 MeV proton irradiations. Two types of SPAD, with and without shallow trench isolation (STI), were designed. According to the experimental results, the leakage current, breakdown voltage, and PDP did not change after irradiation at a DDD of 2.82 × 108 MeV/g, but the DCR increased significantly at five different higher voltages. The DCR increased by 506 cps at an excess voltage of 2 V and 10,846 cps at 10 V after 30 MeV proton irradiation. A γ irradiation was conducted with a TID of 10 krad (Si). The DCR after the γ irradiation increased from 256 cps to 336 cps at an excess voltage of 10 V. The comparison of the DCR after proton and γ-ray irradiation with two structures of SPAD indicates that the major increase in the DCR was due to the depletion region defects caused by proton displacement damage rather than the Si-SiO2 interface trap generated by ionization.