In this work, biogas residues, the remnant of the anaerobic digestion, was used for composting with livestock manure as the co-substrate. It is important for improving the soil quality in China, because the negative influence of biogas residues being utilized directly as organic fertilizer (a mainstream way of disposing biogas residues in China) on the soil could be eliminated or mitigated via composting. The composition of composting substrate has a great influence on the composting process. To explore the influence of the composition of the initial mixtures on the physicochemical properties and spectroscopic characteristics of composts, fifteen co-composting of biogas residue, pig manure and chicken manure, with different material ratios, were carried out. Physicochemical and biological indicators were determined. Meanwhile, spectroscopic methods, such as UV-Vis, synchronous fluorescence and 3D-EEM spectra were used for identifying characteristic spectral parameters companied with FRI and PARAFAC. Therefore