Irradiation structural damage (e.g., radiation tracks, amorphous layers, and vesicles) is widely observed in lunar soil grains. Previous experiments have revealed that irradiation damage is caused by the injection of solar wind and solar flare energetic particles. In this study, cordierite and gabbro were selected as analogs of shallow and deep excavated lunar crust materials for proton irradiation experiments. The fluence was 1.44 ± 0.03 × 10¹⁸ H⁺/cm², which is equivalent to 10² years of average solar wind proton implantation on the Moon. Before and after irradiation, structural damage in samples is detected by slow positron annihilation technology (PAT), Doppler broadening (DB) measurement, focused ion beam (FIB), and transmission electron microscopy (TEM). The DB results showed the structural damage peaks of irradiated gabbro and cordierite were located at 40 and 45 nm. Hydrogen diffused to a deeper region and it reached beyond depths of 150 and 136 nm for gabbro and cordierite, respectively. Hydrogen atoms occupied the original vacancy defects and formed vacancy sites—hydrogen atom complexes, which affected the annihilation of positrons with electrons in the vacancy defects. All of the DB results were validated by TEM. This study proves that the positron annihilation technique has an excellent performance in the detection of defects in the whole structure of the sample. In combination with TEM and other detection methods, this technology could be used for the detection of structural damage in extraterrestrial samples.