The present invention discloses a flux linkage compensator, which applies to an UPS system and comprises a load transformer flux linkage observer, a compensation voltage command generator, and a flux linkage command generator. The load transformer flux linkage observer generates a load transformer flux linkage signal. The flux linkage command generator generates a flux linkage command signal. The difference between the load transformer flux linkage signal and the flux linkage command signal forms a flux linkage deviation signal. The compensation voltage command generator generates a voltage compensation signal to make the flux linkage deviation signal approach zero. Thereby, the flux linkage compensator can compensate for the flux linkage deviation occurring in starting the UPS system. Thus, the present invention can perform voltage compensation fast and reliably and inhibit the inrush current effectively.