Stone buildings exposed to natural environment inevitably subject to various factors. Among which, biodeterioration caused by bacteria, fungi, algae, lichen, and moss is widespread. The long-term cumulative effect of biodeterioration will lead to irreversible changes in the aesthetic characteristics, physical and chemical properties of stone buildings. Therefore, it is necessary to control the biodeterioration of stone buildings. Here, we summarized four traditional methods including heat shock treatments, laser and ultraviolet radiation, application of biocides, and presented typical examples. We analyzed several emerging techniques, such as synergistic effect of physical and chemical methods, plant extracts and nanomaterials biocides, and reviewed their advantages, disadvantages as well as applicability. Aiming to provide a reference for the research of biodeterioration prevention and conservation of stone buildings, we discussed the preventive methods for biodeterioration of stone building and the assessment methods to test the effects of such methods, and prospected the future research direction.