In order to explore the mechanism of the microbial weathering of rock, study the covering green process on rocks and improve the ecological environment, the soil forming effect of weathering granite, gneiss and sandstone was studied. Using ICP-OES and SEM method, the species and capacity of metabolites produced by Bacillus mucilaginosus in the fermentation process, concentrations of various elements released from the granite, gneiss, and sandstone and rock surface morphology were assessed. Results showed that metabolites such as organic acids, amino acids and polysaccharides formed by the B. mucilaginosus had significant differences among three types of rocks, concerning their quantities, granite > gneiss > sandstone; metabolites mentioned above could destroy the structure of the rock, which released many oxides. According to the amount of oxides leached from the three kinds of rock fermentation liquid, more oxides such as SiO2, Na2O, P2O5, Fe2O3, Al2O3, CaO, K2O, MgO, TiO2 were dissolved from the fermentation liquid of the granite. MnO was dissolved in the highest quantities in the fermentation broth of gneiss, more than that of granite and sandstone. The result indicated that the B. mucilaginosus had an obvious weathering effect on three kinds of rocks, especially on the weathering ability of granite.