A usable, software and hardware based method of calibrating crystal frequency was introduced. The output frequency can be tuned exactly by this method, so that the system crystal frequency can be calibrated online without hardware disassemble. The method had improved the efficiency of frequency calibrating. The calibration system was very precise, calibration error caused by calibration software and hardware was 1.5×10-13, which can satisfied most communication system. This method can be applied broadly in communication, radar, frequency synthesizer, and so on.