A method of calibrating an offset of a pressure sensor, by which an offset of a sensing value of a pressure sensor, which detects a pressure of hydrogen in a fuel cell system, is accurately calibrated. The method includes receiving, by a controller, a sensing value of a pressure sensor which detects a hydrogen pressure in a state where a hydrogen supply starts after a start of a fuel cell system; counting, by the controller, a time for which the sensing value of the pressure sensor increases from a first pressure P1 to a second pressure P2; calculating, by the controller, an offset value corresponding to the counted time by use of stored setting data; and calibrating, by the controller, a subsequent sensing value of the pressure sensor by the calculated offset value in real time when the offset value is calculated.