Provided are a method and system for correcting an offset of a hydrogen pressure sensor. The method includes constantly supplying the hydrogen to the fuel cell stack, determining whether an offset of the hydrogen pressure sensor needs to be corrected based on a stop time before the fuel cell stack starts and a magnitude of an output voltage of the fuel cell stack, calculating an offset correction value when the offset of the hydrogen pressure sensor needs to be corrected, and correcting the offset of the hydrogen pressure sensor and performing the starting of the fuel cell stack.