The long stability of atomic clock can be improved by using the second signal of timing receiver to tame the atomic clock. The frequency difference data of rubidium clock is imprecision caused by the various noise influences on the receivers, so a Kalman filter algorithm applied to the frequency calibration system is designed in this article. This algorithm is validated by using FPGA embedded ARM processor. According to the data filter processing, the satisfied frequency difference is gained to calibrate the rubidium atomic clocks.