Active flap is an advanced aerodynamic measure that can effectively increase the flutter performance of flexible bridges, but its control mechanism is still confusing due to the complex phenomenon of aerodynamic interference between the deck and flaps. This study proposes an assessment method to clarify the flutter control mechanism of the deck‐flap system by the computational fluid dynamics (CFD) method and quantifies the contribution of the aerodynamic damping from the active flaps. It is found that the composition of active flap to the improvement of flutter performance can be divided into torque effect and interference effect. Also, the torque effect of the flaps mainly provides equivalent positive aerodynamic damping ratio under effective control parameters, but the interference effects with the deck and two flaps are not the same, and the mutual interference effect between the two flaps is very weak. For the purpose of investigating the aerodynamic interference influence between the girder and flaps, the research further discussed the impact of the distance between the deck mounting position and the bridge girder on the system flutter performance. As the distance increases, the flutter performance of the system gradually improves. Also, the torque effect of the leading and trailing flaps will increase with distance. However, the interference effects of the flaps on both sides show different rules. In total aerodynamic damping ratio of the deck‐flap system, the torque effect accounts for about 70% and interference effect accounts for 30%. As the distance increases, the torque effect gradually becomes stronger and the interference effect gradually weakens.