Cyanobacteria after outbreak and being randomly distributed produced microcystins, polycyclic aromatic hydrocarbons, harmful gases and other toxic substances. In this paper, the process of cyanobacteria decaying was simulated in laboratory, and the changes of organic elements, chloroform extracts A, saturated hydrocarbons and aromatic hydrocarbon during decaying of cyanobacteria had been surveyed. On this basis, we discussed the countermeasure of aromatic hydrocarbons and other toxic substances produced from the accumulation cyanobacteria. Results showed that after 1-month aerobic and 1-month anaerobic decaying, the contents of total aromatics and polycyclic aromatic hydrocarbons in cyanobacteria were decreased to the lowest. Besides, the anaerobic treatment increased the content of total aromatics slightly. The longer the action time of aerobic, the higher content of saturated hydrocarbons, and to the highest in cyanobacteria after 3-month aerobic decaying. N-alkanes will occur relatively strong C-C bond cleavage process, mainly generated small molecules gaseous hydrocarbons. Therefore, we argued that the cyanobacteria, which after 1-month aerobic and 1-month anaerobic decaying, was more suitable for organic fertilizer resource utilization in a pool, then the gas collected for combustion; the cyanobacteria after 3-month aerobic decaying was more suitable for bio-energy. Accordingly, we proposed that monitoring the humification process and to control the formation of harmful ingredients relying on the fluorescence intensity of phycobiliprotein and chlorophyll.