The adaptive phase shift compensator is introduced to estimate the frequency difference of arrival (FDOA), by aligning the time-varying phase shift adaptively. According to the different computation methods, two estimation algorithms，the algorithm based on time average and the algorithm based on linear fitting，are proposed by using adaptive compensation factors. The estimator based on time average is asymptotically unbiased, with controllable error, small mean square error and low computational complexity. Simulation results also show that the performance of the algorithm based on linear fitting is close to CRLB when signals’ SNR are more than -3 dB.