The invention discloses a spacecraft propellant in-orbit filling system and a spacecraft propellant in-orbit filling method. A technology of performing primary exhaust and then performing pressurized filling is adopted, a target conduit head and a filling conduit head do not need simultaneous connection of a gas path and a liquid path, and only a single liquid path is used for connection, so that a docking mechanism is simplified; a supplementary spacecraft is capable of performing pressurized filling without a mounting pump, not only can an attitude disturbing torque generated by rotation of a motor in the pump be avoided, but also the boost pressure during filling is reduced, and the task reliability is improved; before filling, a measure of performing pressure relief on the target spacecraft till reaching a pressure which is below a propellant saturated vapor pressure is adopted, thereby ensuring that the filling rate of the target spacecraft achieves a higher level; in addition, the system has a reusable characteristic; the supplementary spacecraft can be used for performing in-orbit supplement on multiple targets or one target for multiple times, so that a foundation for further implementing in-orbit filling service is laid.