This paper aims to investigate the phenomena and the mechanism of the interaction between Bacillus pumilus and Ca-montmorillonite. SEM results showed that a large number of Bacillus pumilus attached to and wrapped up the surface of Ca-montmorillonite. The content of organic acids of the Bacillus pumilus-Ca-montmorillonite system decreased obviously after joining the Ca-montmorillonite. XRD results showed that the interlayer spacing of Ca-montmorillonite increased, and diffraction peak of 001 exhibited passivation after interacting with Bacillus pumilus. FTIR results showed that peaks assigned to soil bacteria appeared, and peaks of the structural groups of Ca-montmorillonite exhibited blue-shift or red-shift as well. Verification by second derivative FTIR spectroscopy analysis is that Ca-montmorillonite really shows the vibration of other group assigned to soil bacteria. It is thus inferred that there is a preliminary possibility that the metabolic products of soil bacteria enter the interlayer space of Ca-montmorillonite. The result obtained by the authors will provide a new basis for the mechanism of the interaction between mineral and microorganism.