Three intermittent aeration moving bed biofilm reactors (IAMBBRs) with the cycles of oxic and anoxic conditions of 5 h/1 h, 3 h/3 h, 1 h/5 h and a continuous aeration MBBR (CAMBBR) were operated simultaneously to observe the similarities and differences between intermittent aeration and continue aeration during startup stage. Confocal laser scanning microscopy (CLSM) was adopted to study the process of biofilm formation. The IAMBBR accelerated the startup of MBBR effectively by enhancing the rate-limiting step of biofilm formation. The microbes tended to secrete polysaccharide preferentially after attachment, and the primary genus varied from aerobic bacteria to anaerobic bacteria with the reduction of aeration time and the dominant denitrifying bacterial genus also changed. Biomass concentration and the protein/polysaccharide (PN/PS) ratio of biofilm were the highest in the mode of 3h/3h, and Sphaerotilus, Brevifollis, and Saccharibacteria_generaincertaesedis were the dominant genera. In brief, the intermittent aeration could accelerate the startup of MBBR effectively.