The Goal-Oriented methodology (GO methodology) is an effective method for the reliability analysis of complex systems. It is especially suitable for the reliability analysis of multi-state complex systems containing the actual logistics, such as current, airflow and liquid flow. In order to solve the limitation that the GO methodology is not suitable for the reliability analysis of the system with feedback loop, the Boolean algebra idea is introduced to construct the Boolean operation formula of the feedback loop. In this paper, a certain type of civil aircraft flap hydraulic system with feedback loop is taken as the research object. According to the structural schematic diagram of the flap hydraulic system, the GO model of the flap hydraulic system is established. Next, the GO calculation is carried out to obtain the reliability of the flap hydraulic system. The comparison between the system reliability without feedback loop and that with feedback loop proves that the GO methodology with feedback loop is more accurate. The reliability of the system is analyzed by using the fault tree analysis (FTA) method, and the GO methodology with feedback loop is compared with the FTA method to verify the availability and correctness of the GO methodology in the reliability analysis and safety evaluation of aircraft flap hydraulic system.