Fractional pyrolysis and one-step pyrolysis of natural algae Cyanobacteria from Taihu Lake were comparatively studied from 200 to 500 degrees C. One-step pyrolysis produced bio-oil with complex composition and low high heating value (HHV <=,30.9 MJ/kg). Fractional pyrolysis separated the degradation of different components in Cyanobacteria and improved the selectivity to products in bio-oil. That is, acids at 200 degrees C, amides and acids at 300 degrees C, phenols and nitriles at 400 degrees C, and phenols at 500 degrees C, were got as main products, respectively. HZSM-5 could promote the dehydration, cracking and aromatization of pyrolytic intermediates in fractional pyrolysis. At optimal HZSM-5 catalyst dosage of 1.0 g, the selectivity to products and the quality of bio-oil were improved obviously. The main products in bio-oil changed to nitriles (47.2%) at 300 degrees C, indoles (51.3%) and phenols (36.3%) at 400 degrees C. The oxygen content was reduced to 7.2 wt% and 9.4 wt%, and the HHV was raised to 38.1 and 37.3 MJ/kg at 300 and 400 degrees C, respectively. Fractional catalytic pyrolysis was proposed to be an efficient method not only to provide a potential solution for alleviating environmental pressure from water blooms, but also to improve the selectivity to products and obtain high quality bio-oil.