An Unmanned Aerial Vehicle (UAV) controller with high safety is a critical factor for ensuring the integrity of UAV combat, which is capable of regulating the UAV’s flight performance within a secure operational boundary.To design a safety controller for the UAV, analysis is made on the closed-loop control system of UAV, and the nonparametric prediction error estimation method is used to identify the actuator modules in the system, thus to demonstrate that the identified model is unbiased with the actual model. Furthermore, the concept of UAV safety is clarified, and a safety controller for UAVs is designed based on the identified model of the closed-loop control system.Finally, taking the pitch channel of UAV flight attitude angles as an example, simulation is made to validate the performance of the safety controller.Experimental results affirm the effectiveness of the UAV safety controller, which can regulate the UAV’s flight performance within a safe range, thereby ensuring the safety of UAV flight.