Many aerial applications require unmanned aerial systems operate in safe zones because of the presence of obstacles or security regulations. It is a non-trivial task to generate a smooth trajectory satisfying both dynamic constraints and motion limits of the unmanned vehicles while being inside the safe zones. Then the task becomes even more challenging for real-time applications, for which computational efficiency is crucial. In this study, we present a safe flying corridor navigation method, which combines jerk limited trajectories with an efficient testing method to update the position setpoints in real time. Trajectories are generated online and incrementally with a cycle time smaller than 10 μs, which is exceptionally suitable for vehicles with limited onboard computational capability. Safe zones are represented with multiple interconnected bounding boxes which can be arbitrarily oriented. The jerk limited trajectory generation algorithm has been extended to cover the cases with asymmetrical motion limits. The proposed method has been successfully tested and verified in flight simulations and actual experiments.