The contribution of microbial residues formed on lignin and cellulose to the formation of humus (HS) was investigated. The microbial residues formed by Aspergillus niger (A. niger) in the cultures of cellulose and lignin in a fluid medium were structurally characterized by elemental analysis, differential thermal analysis (DTA), FTIR spectroscopy and CP/MAS 13 C NMR spectroscopy. Compared to cellulose itself, the microbial residue from cellulose contains more aromatic compounds and N-containing compounds and fewer carbohydrates and carboxylic compounds. A. niger improved the thermal stability and aromaticity of the cellulose. However, compared with that on lignin, more N-containing compounds, carbohydrates and carboxylic acid derivatives and less aromatic material were found in the microbial residue from lignin. Regardless of whether the carbon source was cellulose or lignin, A. niger utilized the N in the fluid medium to synthesize its own cells, and eventually, they could transfer the N into the microbial residue; in addition, the O-alkyl species dominated over the alkyl and aromatic compounds in the microbial residue. Although the molecular structures of the components of the microbial residue from lignin tended to be simpler, they were more alkylated, more hydrophobic and less aliphatic than those from cellulose. During culture with A. niger, the cellulose underwent degradation and then a polymerization, which led to an increased degree of condensation but a lower degree of oxidation, providing essential precursor substances for HSs formation. However, lignin underwent oxidative degradation. The microbial residue from lignin had a lower degree of condensation and a higher degree of oxidation.