Chinese culture has a long history and has left us a lot of stone relics with historical, artistic and cultural values. In recent years, the Chinese Government has established requirements for the protection and utilization of cultural relics and also for the protection and inheritance of cultural heritages. Therefore, more and more attention is also being paid to protection issues of stone relics. Besides human destruction and surface contamination, more damage to stone relics is caused by natural weathering, erosion and corrosion due to factors such as sunlight, rain, wind, sand, surface water, underground water and earthquake, etc. We studied the diseases of the outdoor stone cultural relics, Yanghuayan Lithoglyphs (one of the 6th batch of National Key Cultural Relics Protection Units) using two nondestructive methods, namely surface nuclear magnetic resonance (SNMR) and ground penetrating radar (GPR). The SNMR method successfully detected distribution of water in the rock mass where the lithoglyphs are attached. The development of karst and fractures of the rock mass was detected by the GPR method. The results indicate the development of karst and rock mass fractures and also show that the karst and fracture zones of some parts have become a gathering place or circulation channel for underground water, which results in severe threats to the lithoglyphs. The results of these two methods are mutually verified and thus provide reliable data for the protection and disease management of the Yanghuayan Lithoglyphs.