The flight control computer subsystem is the calculation and control core of the flight control system, which affects flight safety. Using BIT for fault detection and positioning can significantly improve the safety of the flight control system. In the current stage of BIT design research, the system level tends to focus on top-level functional requirements, while the BIT research of computing devices focuses on the software and hardware of general-purpose computers. The requirements transmission and traceability from flight control systems to computer subsystems are not strong, and there is a lack of research on the BIT design process of flight control computer subsystems based on system engineering. By analyzing the architecture of the flight control computer subsystem, its general components were identified. Based on this, BIT design research was carried out, the classification and characteristics of BIT were analyzed, general requirements for BIT design were proposed, and the BIT design process for the flight control computer subsystem based on system engineering was designed. Starting from the functional requirements of the flight control system, this paper discusses in detail the initialization, working mode conversion, testing items, execution timing, and design methods and principles of BIT project test with high correlation with the flight control system functions, and analyzes the design methods for fault prediction and health management, as well as measures to reduce false alarms. The flight control computer subsystem BIT design using this design process and detailed design principles has been validated through ground comprehensive tests.