Drived by the soil microorganisms, the decomposition and transformation of cellulose plays an important role in the formation of humic substances. The techniques of infrared spectrum combining with element analysis were adopted to compare the structural differences of humic-like substances (HLA, humic-like acid; Hu, humin) extracted from the microbial residues formed in the liquid shake-flask culture (70 days), in which the single fungi (Trichoderma viride, Penicillium and Aspergillus niger) and mixed strains participated. The results showed that: (1) The combination of two techniques could clarify the molecular structure of HLA extracted from the microbial residues, however, it remained to be further discussed in terms of analyzing the structures of Hu; (2) Trichoderma viride was beneficial to the condensation of HLA extracted from its microbial residue, but Penicillium was more favorable to the degradation of HLA. (3) The oxidative degradation of HLA fractions extracted the microbial residues was implemented by Penicillium and mixed strains. Both of the mixed strains and Aspergillus niger were helpful to transfer the inorganic N compounds from the culture media into the organic N components of HLA and Hu extracted from the microbial residues, simultaneously increase their amino C contents and then provide the indispensable N source for the humification process.