Abstract: The reconfigurability of SRAM-based FPGA has been used for fault diagnosis in aerospace applications. In general, fault diagnosis adopts coverage testing and multiple iterations of "bitstream loading and testing". The growing scale of FPGA's bitstream requires longer time on coverage testing and more storage space for bitstreams, which is hardly feasible in aerospace electronic systems. Analyzing bitstream and summarizing the relevant multi-group calculation formulas, including information such as cell coordinates, row addresses, major addresses, minor addresses, etc. which helps in diagnosing the bitstream of tile (the basic unit) and confirming the information of tiles' internal structure configurations. Based on the formulas, a method of fault diagnosis is proposed through comparison tests in FPGA undertest. This method divides FPGA's resources into small grids, copies the bitstream from area undertest to a adjacent location, organize testing structures based on linear feedback shift registers, and make comparisons grid by grid for fault diagnosis. Furthermore, this paper optimizes the grid size for fault diagnosis. The optimization demonstrated on XC7VX330T shows that the time of fault diagnosis is less than 619 seconds. Compared to existing fault diagnosis methods, external storage space is not required, which benefits electronic systems with reducing loads in aerospace applications.