The start-up tests and micro-ecological conditions of treating cyanobacteria in the Taihu Lake by an anaerobic baffled reactor (ABR) filled with soft filler have been studied. The results showed that, under the following conditions of dosing seed sludge, continuous operation by improving the load by steps after 40 days, the cyanobacteria could be successfully processed. In the process of start-up, the COD (chemical oxygen demand) removing rate was about 75%, and the gas production rate was about 65.9mL/L.d. In addition, the reduction rate of microcystins reached 90%. The soft filler played a key role in treating cyanobacteria successfully by the improved Anaerobic Baffle Reactor. It was found that the soft filler had function in forming biofilm and training granular sludge in the reactor. In addition, it is beneficial in promoting the more reasonable space distribution of the microbial communities in the compartments. The protease content of the granular sludge in ABR decreased and coenzyme F420 content increased progressively along separation chambers. It is consistent with the quantity of archaea and bacteria along the separation chambers in the reactor.