Abstract: To resolve the problem of future air traffic management under great traffic flow, high density, and small separation condition, a hybrid control system structure for flight confliction supervisory control is proposed.Firstly, a set of kinematic equations for the aircraft are proposed according to different flight stages. The confliction hyper-surfaces are defined based on air traffic control rules to forbidden the trajectory of the system composed by multiple aircrafts to cross it, and the crossing events can be recognized by a designed supervisor. In addition, the flight confliction discrete controller is designed according to resolutions available for air traffic controller to decide which control input should be applied. The continuous control input vector is derived under the condition that the difference value of confliction hyper-surfaces keeps negative in a resolution period, which keeps the air traffic system in the safe space. Case study proves that the method based on hybrid system theory can detect potential conflictions and resolve them in advance.