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There are many grottoes of the Song and Jin Dynasties in northern Shaanxi, the Qingliangshan grottoes of Yan’an is typical representatives. Due to the influence of environmental and geographical factors, the microbial of the Qingliangshan grottoes have caused the surface weathering, pollution or discoloring of cultural relics, as well as the potential dangers, which have caused some damage to the grottoes. This paper based on the investigation of harmful microbial samples on the surface of the grottoes of Qingliangshan in northern Shaanxi Province. Using microscopy and molecular biology to analyze microbial communities, Understand the influence and harm of microorganisms on grottoes, then to display and publicize with graphical information, to make readers understand the influence of microbial disasters on the grottoes and further attract people’s attention. It is form a consensus on protecting the material and cultural heritage of grottoes and promote the inheritance of traditional Chinese culture.