The invention discloses an unmanned-aerial-vehicle height measurement control system based on fault-tolerance processing and a control method. The unmanned-aerial-vehicle height measurement control system comprises a height meter module, a satellite navigation module, an inertial measurement module and a computing and processing module. The height meter module is used for measuring the distance of an unmanned aerial vehicle to the ground in real time; the satellite navigation module is used for receiving and processing satellite signals in real time and measuring the flight position and the direction of the unmanned aerial vehicle; the inertial measurement module is used for measuring the attitude angular velocity and the accelerated velocity of the unmanned aerial vehicle in real time; the computing and processing module is used for receiving data of the height meter module, the satellite navigation module and the inertial measurement module in a parallel mode and computing and obtaining height measurement data. By means of the unmanned-aerial-vehicle height measurement control system based on fault-tolerance processing and the control method thereof, the conditions of the fault of a height meter or the fault of satellite navigation or the faults of a height meter and satellite navigation can be synthetically processed, and the high stability of the unmanned aerial vehicle is guaranteed through the control system to a maximum limit.