The conservation of historic stone buildings and sculptures is receiving growing attention because of weathering. Now, the techniques for stone conservation are primarily achieved through the use of organic coating treatments. Although some defects of organic protective materials have been recognized, the further shortcoming is still short of awareness. Here we show our investigations of the side effect of organic coating treatments. Some kinds of common stones, including sandstone, tuff, granite, dolomite and marble, were selected as protected objects. Organic silicon compounds were used as protective coatings. The artificial weathering, including salting, freezing and heating, was designed. The treated stones’ decaying was investigated. The results reveal that the treated stone decaying is aggravated. Moreover, the destruction mechanism has been discussed.