Abstract: SRAM-based FPGA microsystems with SiP(System in a Package) packaging technology are widely used in the aerospace applications. Due to the complex packaging structure of microsystems, the most traditional failure analysis equipment and methods are restricted. For the reliability of microsystem devices, such as difficult fault diagnosis and complex testing process, a common fault analysis is conducted. In depth analysis and summary are conducted on the generation mechanism of typical faults such as inherent defects in SRAM configuration and abnormal refresh circuit in FPGA internal configuration. Based on theoretical analysis and observed problem phenomena, testing methods for configuration reply verification and comparison, as well as parameter consistency control for the current of auxiliary power supply V_CC,AUX are proposed, which can effectively improve test coverage. By utilizing appropriate testing methods and data analysis techniques, the failure analysis mechanism and location can be accurately identified. This has important significance for the application and screening coverage of SRAM-based FPGA microsystems for future aerospace applications.