Reliability is an inherent attribute of a system through optimal system design. However, during the aircraft system development process, the reliability evaluation and system function design efforts are often disconnected, leading to a divide between reliability experts and system designers in their work schedule. This disconnect results in an inefficient aircraft system reliability optimization process, known as the two-skin phenomenon. To address this issue, a three-state space model is proposed. Firstly, an analysis was conducted on the relationship between the system function architecture developed by the system designers and the reliability evaluation performed by the reliability experts. Secondly, based on the principle of function flow, the state of failure was categorized into physical failure and non-physical failure. Additionally, a new state of function loss was introduced as the third state for the system, in addition to the traditional states of normal and faulty. Thirdly, through the state of Function loss, an effective integration of system fault modes and function modes was achieved, leading to an optimized system reliability model. A three-state space modeling method was then developed by transforming the system function architecture into a system reliability model. Finally, this new model was applied to an aircraft's rudder and fly-by-wire control system. The results demonstrate that the function architecture at the design stage of the system can be accurately transformed into the new three-state space model. The structure aligns closely with the function architecture and can be effectively utilized in quantitative system reliability calculations. In this way, the process of ensuring system reliability can be seamlessly integrated into the system optimization design process. This integration alleviates the issue of disjointed work between reliability experts and system designers, leading to a more streamlined and efficient aircraft system optimization process.