Flight testing is an essential step to reflect the weak links in aircraft design and manufacturing, which is vital to guarantee the high reliability and long-life operation of aircrafts. Covering many subsections of the airplane, the flight control system (FCS) is a key sub-system for adjusting the attitude of the airplane. This highlights the need for a proper reliability modeling approach during flight testing phase, which is of great importance. To alleviate this issue, this work proposes a reliability modeling and analysis method for the FCS in flight testing phase based on the belief reliability theory. First, based on control theory and mechanical principles, the performance equations of the FCS are established. On top of this, the uncertainties during the production and manufacturing processes are analyzed, and a reliability measurement equation for the FCS is proposed. The proposed method utilizes physical and data information from flight testing phase to support the design and maintenance of the FCS. And a numerical study is used to measure the reliability of the FCS.