The GPS signal calibrating crystal oscillator frequency source can output time frequency signal with high accuracy. However, when the GPS signals can not be received due to some factors, the system can only rely on the crystal oscillator to keep a standard output at a certain frequency. Influenced by aging and other factors, drift may arise in the output frequency of crystal oscillator. To correct and compensate for the output frequency drift at the time when losing the GPS signal, an algorithm is proposed based on ARMA model for maintaining the frequency source accurate. Through analyzing the historical calibrating data, the crystal oscillator performance degradation model is established, thus to implement the compensation for the system output frequency, and keep a relatively stable and highly accurate output frequency. The proposed method is applied to a GPS signal calibrating crystal oscillator frequency source, and the result shows that the average relative error of the system output frequency can remain at 1. 80% after the GPS signal lost shortly.