The invention discloses a reconfigurable integrated measurement-control, navigation, flight control system and a reconstruction method thereof. The system comprises a radio frequency front end and an information processing platform. The information processing platform consists of a flight control unit, a function reconstruction unit, a measurement and control receiving-transmitting management unit, and a configuration management unit. When the carrier height is in an acting range of a satellite navigation system, the system works in a stand-alone working mode; the function reconstruction unit loads a navigation processing program; and the system completes measurement and control, navigation and flight control functions. When the carrier height exceeds the acting range of the satellite navigation system, the configuration management unit reconstructs the function reconstruction unit and loads a flight control back-up program, and a dual-redundancy state of measurement and control, navigation, flight control functions is formed, and the system works in a dual working mode. With the reconstruction method, the system functions are optimized; the utilization efficiency of the system hardware resources is improved; and demands of multiple functions, high reliability and low cost are satisfied simultaneously.