This study was carried out on a sequencing batch biofilm reactor which was damaged after successful start-up of reactors with the process of autotrophic nitrogen removal in one reactor. The reasons why the system was destroyed and the change of denitrification performances were systematically analyzed. The controlling strategy speeding the recovering process of the system was also discussed based on the experimental data. After the damage of biofilm and activated sludge flocs in the system, serious nitrite accumulation occurred and nitrite concentration in the effluent of the system was about 70mg/L. The removal rate of total nitrogen fell from 78.6% to 13.1%. The short-term adjustment of DO (dissolved oxygen) concentration had no distinct improvement for the system's nitrogen removal efficiency. In this condition, a two-step strategy, improving the reactor's performance after prompt bilofilm formation with high DO concentration was suggested. It was also showed that the DO concentration should be adjusted timely according to the changes of biofilm thickness and flocs diameter. The biofilm formed again about 22d when DO concentration was controlled at 1.6~2.2mg/L, the removal rate of total nitrogen reached about 80% under this strategy.