With the development of aviation industry around the world, unmanned aerial vehicles (UAVs) are broadly applied in modern warfare and civilian fields, which induces a big boom in the number of aircrafts, thus posing a great threat for flight security with the increasing aircraft density in the sky in the near future. Although current researches and methods can deal with the UAV safety problems well at some extent, the effectiveness of them is greatly reduced when the UAV is in a highly antagonism and harsh environment. In this work, the autonomous safety control method for the UAV system is researched and explored from the need of improving the operational security of UAV system. UAV safety control method based on cognition-guidance refers to that the UAV can rely on perceptual and cognitive computing functions of the UAV system during the flight guidance to perceive and identify the forthcoming or ongoing security risks and to generate a correct evasion strategy. Cognition-guidance is a specific application of the cognitive computing. The safety connotation of the UAV and the research status of safety control are firstly analyzed, then, the relationship between the guidance and human cognition is discussed, and the UAV safety control method based on cognition-guidance is proposed. Besides, the UAV anti-collision control strategy is designed, and taking the two UAVs anti-collision control mission as an example, the simulation research for the UAV safety control method based on cognition-guidance is studied. And the simulation results have proved that the method is effective.