Aerobic composting experiments were conducted using lincomycin mycelia wastes (dreg) and manure (T), using sewage sludge with manure as a control (CK). High performance liquid phase methods and high throughput sequencing were used to determine the concentration of lincomycin residue and to characterize the microbial community. The results showed that lincomycin was reduced significantly, with the concentration decreasing from 1800 mg·kg to 483 mg·kg , accounting for 73% degradation. In addition, the bacterial community abundance and diversity indices were all lower than that of sludge-manure at the mesophilic and thermophilic phases, because of the high concentration of lincomycin residue in lincomycin mycelia dreg. By contrast, the fungal community abundance and diversity indices showed the reverse, due to the high content of organic matter and nitrogen in lincomycin mycelia dreg. Therefore, the microbial communities were greatly different between T and CK treatment with the domain genera of , , , , , and in