The space-borne rubidium atomic frequency standards(RAFS) play a critical role in many space systems. Their performance and reliability will greatly influence the functions of these systems. The failure mode and effects analysis (FMEA) is applied in the space-borne RAFS to identify and rectify the failures during its development and design stages. The basic principle of the space-borne RAFS and its framework diagram are introduced. A certain space-borne RAFS is divided into six subsystems and its reliability block diagram is depicted. Each subsystem is analyzed by FMEA and a part of the FMEA table of physics package subsystem is presented as an example.