The catalytic action of clay minerals have an important contribution to the formation of humic substance (HS) from the lignin. In order to elucidate the relationship among the microorganisms, lignin and clay mineral effectively and reveal the structural characteristics of mineral-microbial residues, the method of liquid shake flask culture was adopted in this article, the lignin serving as the sole C source, through the addition of kaolinite or montmorillonite to start the liquid culture of 110 days after inoculating the multiple strains, and then the mineral-microbial residues were dynamically collected and their characteristics were studied by FT-IR and SEM techniques. The results were as follows: The kaolinite particles were mostly formed from the crimp of tube-like material edges. After its participation in the formation of microbial utilization of lignin, much more structures from the fine particles of mineral-microbial residues were further aggregated and they were more integrated, in the process the structures like short tubular were increased, but the overall state still maintained the structural characteristics of hydro-kaolinite. Under the initial culture with a rich variety of nutritive elements, the kaolinite could promote the microbial reproduction, which could make a large number of microorganisms gathered on the kaolinite surface and the Si—O and Si—O—Al bonds were masked. During the process, the proportion of aliphatic C structure of mineral-microbial residues were increased; The H bonds could be formed from the conjunction of multiple O-containing functional groups of high-molecular polysaccharides and the hydration shell of kaolinite at the multiple sites. The formation of H bonds had significant effect to stabilize the lignin and its degradation products from the kaolinite. With the culture, the proportion of aromatic C structure and the polysaccharides content were gradually increased, and then the microbial residues masked on the surface of kaolinite were utilized again by the multiple strains with active ability, which could make its Si—O—Al bond reappeared; Montmorillonite was mostly composed of round particles, and the dissolution was caused by the microbial inoculation on its surface, which could make the granular structures broken and produce much more fragmented structures. Compared with 10 days, the polysaccharides of mineral-microbial residues obtained from the culture of 30 days were increased, which could make the absorption peak at 1 034~1 038 cm-1 assigned as the Si—O—Si and Si—O bonds overlayed and strengthened, and then the intensity of absorption peak at 1 034~1 038 cm-1 was weakened due to the association of polysaccharides with hydroxyl of montmorillonite surface, and simultaneously the intermolecular H bonding occurred, which was the main mechanism for the interaction of montmorillonite, microorganisms and lignin and their formation of mineral-microbial residues. The ability to stabilize organic C from the kaolinite was more than montmorillonite, which was easier to promote the formation of HS precursor substances.