A strain of silicate bacteria isolated from the surface of bauxite was chosen to carry out a study on the microbial degradation of bauxite with complicate mineral compositions. Bauxite was incubated in nitrogen-free medium containing silicate bacteria. During shaking incubation, the concentrations of main impurity elements containing in bauxite such as aluminum, silicon, ferrum, calcium were measured in the weathering medium, and bauxite samples were collected and analyzed by X-ray diffraction and electron microscope. The results showed that the bacteria indeed eroded the surface of bauxite, and obviously formed the mycelium-mineral complex between silicate bacteria and mineral powder with the extension of shaking culture time. Furthermore, silicate bacteria selectively degraded different minerals containing in bauxite due to difference in mineral crystal structure.