The pyrite oxidation is crucial to the overall black shale oxidation process. A. ferrooxidans was documented an effective oxidation ability on pure pyrite, but its role in black shale oxidation is unclear. In this study, a comparative study of acid solution and A. ferrooxidans on the micro-surface characteristics at the initial stage (7 days) was conducted on black shale slices, a comprehensive approach combining the micro-morphologies, micro-structures, micro-environmental pH and micro-surface elemental content were investigated by using polarizing microscopies, SEM, fluorescent staining and EDX line scan analysis. The pyrite oxidation rate was employed to the index for black shale oxidation degree, and analyzed by XRD, aqueous pH, oxidation-reduction potential (ORP), ferrous and ferric ions concentrations measurement. The results show that the micro-surface characteristics are different in acid solution and A. ferrooxidans groups, which significantly impact the pyrite oxidation rate. A. ferrooxidans promote the jarosite formation and elemental C accumulation on the rocks micro-surface, which is assumed to inhibit further reactions. Two reaction phases named "pyrite oxidized phase" and "jarosite formation phase" are proposed to occur in the initial stage of A. ferrooxidans oxidizing black shale. These findings provide experimental data to evaluate the micro-surface reactions during black shale oxidation process.