Microbial mineralization (corrosion, decomposition, and weathering) has been investigated for its role in the extraction and recovery of metals from ores. Here we report our application of biomineralization for the microbial enhanced oil recovery in low-permeability oil reservoirs. It aimed to reveal the etching mechanism of the four Fe(III)-reducing microbial strains under anaerobic growth conditions on Ca-montmorillonite. The mineralogical characterization of Ca-montmorillonite was performed by Fourier transform infrared spectroscopy, X-ray powder diffraction, scanning electron microscopy, and energy-dispersive spectrometry. Results showed that the microbial strains could efficiently reduce Fe(III) at an optimal rate of 71%, alter the crystal lattice structure of the lamella to promote interlayer cation exchange, and efficiently inhibit Ca-montmorillonite swelling at a rate of 48.9%.