The distributed system architecture with openness and comprehensive control features has been successfully applied in the development of flight control systems for advanced fighter jets. However, current fault-tolerant control for flight control systems mainly targets centralized flight control systems in third-generation aircraft and cannot be directly applied to flight control systems with a distributed architecture. Therefore, this paper will study fault-tolerant design for flight control systems based on distributed system architecture. Firstly, this paper introduces the typical system architecture of distributed flight control systems and the objectives of their fault-tolerant design. Secondly, based on the operational timing and working mode characteristics of the distributed system, a time-based fault-tolerant design is conducted. Finally, based on the composition and system architecture characteristics of the distributed system, a system architecture-based fault-tolerant design is carried out. Through the analysis of the operational timing, working modes, composition, and system architecture characteristics of the distributed system, this paper identifies the key entry points and design principles for fault-tolerant design of distributed systems, and explains the solutions, methods, and engineering practice effects of the fault-tolerant design scheme.