A space electric propulsion system and a xenon filling method therefor are provided, suitable for a filling process of an electric propulsion system using high-purity xenon as a working medium. By reasonably designing a filling process, the precision of a xenon filling amount is ensured, and xenon filling can be performed without weighing the whole spacecraft. This method features a simple and efficient filling device, short preparation time, precise and controllable filling process, as well as safety and convenience, which can effectively meet the requirements for a high-purity xenon rapid filling task of a satellite.