Outdoor stone heritage accounts for a large portion of UNESCO World Heritage Sites and is an essential carrier of the ancient civilization of our society. Unfortunately, they usually suffer from serious biodeterioration by diverse microbial colonizers, especially when the environment is available. As microbial communities evolve with the environment, it is difficult to diagnose the bio-deteriogens and biodeterioration processes accurately. Here, we used an integrative high-throughput sequencing and comparative metabolomic approach to unravel the biodeterioration of the Leizhou Stone Dog monuments. Contrary to our initial hypothesis of congruence between the biodeterioration of the monuments in the same yard, we observed divergent physicochemical features of the sedimentary soils at the bottom of the monuments, highlighting the need for a nuanced framework capturing the keystone microorganism–metabolite interplay. The divergence and similarity of the composition of microbial biofilms colonizing the monuments indicated that photoautotrophic bacteria (e.g., Leptolyngbya, Chroococcidiopsis, and Chloroplast) and nitrifying archaea (e.g., the family Nitrososphaeraceae) and/or bacteria (e.g., Massilia and Bacillus) are the keystone taxa governing the biodeterioration processes. Further, the correlation between the keystone taxa and physicochemical properties confirmed the consistency of the observations of the keystone metabolisms involved in the biodeterioration processes. Our study highlights the necessity of a case-by-case diagnosis of the keystone taxa and metabolisms before any therapy, advancing the conservation science of cultural heritage.