In GPS/INS/barometer navigation system for UAV, two procedures were proposed in order to set three reference parameters for the pressure altitude of QNH or QFE settings, using the navigation data from on-board system alone. These procedures yield required the reference parameters through mathematical process with the altitude and the atmosphere properties measured for a short duration of flight, of which a special pattern is requested according to the selected procedure. Dependency only upon the on-board navigation data can eliminate a requirement for the atmospheric measurement system in the ground support system and can expand a flight boundary to a remote area where the ground support is not available. Especially the procedure with the regression method uses altitude and pressure but temperature to produce the three reference parameters. No need of temperature measurement for the pressure altitude system can simplify the on-board air data system.