In the present work, the acidophilic and thermophilic strain Acidithiobacillus caldus was used for biodesulfurizing coal and bioleaching coal pyrite. The surface characteristics of cells and minerals and the mineral transformation during the coal pyrite leaching process were investigated combined with zeta-potential, FT-IR spectroscopy, scan electronic microscopy and X-ray absorption near edge structure spectroscopy (XANES). The results showed that the coal pyritic desulfurization with A. caldus was about 47% and the total desulfurization was 19%. After processed by cells, there was clear corrosion on the pyrite surface. Coal pyrite and elemental sulfur-grown cells had more hydrophilic functional groups than thiosulfate-grown cells. During the coal pyrite leaching course, the elemental sulfur was the main sulfur speciation but no other secondary mineral components were detected.