2 it was found that bacterial community structure both changed obviously with obvious performance decline in the two digesters. Excessive FAN (> 500 mg· L-1) could change the main bacteria species which degrade protein from Tepidimicrobium and Proteiniborus to Anaerobranca. On the other hand, some carbohydrate and protein degrading bacteria were also inhibited by pH reduction for FAN control, leading to the decline of hydrolysis rates of organic matters. As a result, the shortage of substrate supply for the methanogens weakened the biogas production of the digestion system.