The frequent occurrence of cyanobacterial blooms in eutrophic lakes can lead to a high amount of biomass in aquatic systems, and following cell death, this autochthonous organic matter will eventually decompose. In this study, the effect of temperature and sediment on the chemical composition of cyanobacterial biomass residue was investigated by microcosm experiment. The results showed that the lowest cyanobacterial bloom biomass (CBB) removal efficiency was recorded at 32°C regardless of the presence or absence of sediment. Based on total organic carbon, the CBB removal efficiencies were higher than 90% at 20-29°C but less than 87.0% at 32°C. Pyrolysis gas chromatography mass spectrometry and Fourier transform infrared analysis indicated that organic nitrogen compounds (e.g., carbamic acid monoammonium salt) and polysaccharides (e.g., 2-propanone, 1-hydroxy-) were the main components in the residues. Based on the determined components in the residues under different conditions, unweighted pair group clustering method with arithmetic averages and principal components analysis further suggested that sediment and temperature had obvious influence on the chemical composition of CBB decomposition residues. Considering that cyanobacteria biomass is produced annually in eutrophic lakes, residues from CBB may contribute to the nitrogen/carbon cycles and macro-fauna growth in these ecosystems.