When the UAV performs a low altitude penetration mission, the aircraft is in a low altitude, low-speed, low kinetic energy, and low potential flight state, while facing a complex terrain and surface clutter interference flight environment. This article proposes a low altitude terrain following trajectory control method for unmanned aerial vehicles based on energy protection. The recursive average filtering method and high pass filter are used to filter the radio altitude difference sequence in flat and undulating terrain, and weight is allocated to the current calculation period’s altitude difference. The altitude change rate is used to improve flight quality, and energy protection is applied based on the current flight attitude of the aircraft to avoid aircraft stall. By adjusting the longitudinal control command to adjust the trajectory, low altitude terrain following trajectory control is achieved.