To overcome the drawbacks of phase difference of arrival （PDOA）dual-frequency comparison ranging method, i.e. large frequency selection random and low measuring distance accuracy, the phase difference of arrival in frequency domain (FD-PDOA) dual-frequency comparison ranging method is proposed. Combining with the least square method and linear regression, a mathematic model is built to measure the distance. Simulation results show that the measurement error of PDOA dual-frequency comparison ranging method floats at 50% and 30% at distance 0.5 m and 1.0 m respectively, while the measurement error of FD-PDOA dual-frequency comparison ranging method is reduced to 10% through an overall analysis of the phase difference change characteristics, and the method considerably improve the measuring distance accuracy.