In this study, to address the reservoir injury problem triggered by montmorillonite hydration and expansion in high-temperature sour reservoirs (60℃, pH=6.5) in Shengli Oilfield, high-temperature-resistant silicate mixing bacterium was isolated from in-situ formation water and named as SSB-Mnt, to investigate the coupling mechanism of the modification of the mineral structure of montmorillonite. Through multi-scale characterization by X-ray diffraction analysis (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy-energy spectroscopy (SEM-EDS) and inductively coupled plasma-optical emission spectrometer (ICP-OES) combined with dynamic analysis of the elemental content of the system, it was found that SSB-Mnt synergized with electron transfer through the metabolic production of acid (pH value reduction from 6.6 to 5.5), the reduction of 43.8%～49.7% structural Fe³⁺ in montmorillonite was achieved within 30 days (average Fe²⁺ concentration 0.402 mmol/L). Mineralogical evidence suggests that microbial action resulted in montmorillonite interlayer collapse with a reduction in layer spacing from 1.49 to 1.22 nm, depolymerization of the silica-oxygen skeleton (reduction in the intensity of the Si—O—Si absorption peaks), and the formation of secondary minerals associated with elements Fe, Ca, Ti, and P. In this study, we explored the model of synergistic modification of high-temperature-resistant bacteria and minerals under reservoir conditions, and formulated the formulated medium, which provided a theoretical basis for the microbial anti-expansion technology in unconventional oil and gas reservoirs.