The Fe, Al, Mn oxides play an important role in the catalytic action of lignin being transformed into HS. In order to elucidate the relationship among the microorganism-lignin-Fe, Al, Mn oxides effectively and reveal the structural characteristics of mineral-microbial residues, the culture method of liquid shake flask was adopted in this article, the lignin serving as the C source, through the addition of goethite, bayerite and δ-MnO2 powder 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: goethite had some pine needle structures, and the strips of dark materials were formed and attached to its surface after its participation into the formation of mineral-microbial residues from the microbial utilization of lignin. The apparent structures of goethite were irregular, but its crystal structure had not been changed. The polysaccharides from the multiple strains could exchange with the anions of free hydroxyl groups of goethite, and the proportion of aromatic C structures could be increased. The Fe—OH bond and γ-OH bond of (001) surface were masked due to the microbial thallus covered on the surface of goethite, and the vibration frequency of Fe—O bond was enhanced by the protonation of Fe—OH; The surface structure of bayerite was loose and resembled with the fluff sphere-like substances. After the participation of bayerite in the formation of mineral-microbial residues, its polycondensation effect was obvious, the loose degree was decreased, and the microcellular structure from its surface was reduced. The aluminum hydroxyl vibration frequency of mineral-microbial residues was decreased due to the hydrogen bonding effect, namely the polarity of O—H bond combined with AlOH was weakened. The introduction of lignin could enhance the proportion of aromatic C structure of mineral-microbial residues, but with the culture, its content was decreased first, and then was through the condensation; The surface of δ-MnO2 particles were rough, which could be aggregated in the flocculent or granular form. After the participation in the formation of mineral-microbial residues, the aggregation trend of particles was obvious, the stacking was more compact and its surface structure was more smooth. During the period of 60 days, the crystallinity from δ-MnO2 was affected by the superposition from the microbial thallus and hydrogen bonding, which could reduce the polarity of O—H bond. The increase of —OH content of H2O molecule in the interlayer could produce a superposition effect on the O—H bond, which could enhance the absorption peak intensity of 3 404~3 435 cm-1. The proportion of aromatic C structure of mineral-microbial residues was caused by the association of the hydroxyl groups from the polysaccharides of microbial thallus with the δ-MnO2 through the hydrogen bond and chemical force, but in the process the Mn—O group was masked. The participation of δ-MnO2 could make the mineral-microbial residues produce much more aromatic C structures and provide much more stable C contents for the formation of HS, followed by goethite, while the bayerite was beneficial to the microbial degradation of lignin during the culture of 30~60 d.