To the problem of time delay difference(TDD) estimation of unknown frequency, the paper
describes that a time delay difference estimation method with time delay difference variance weighted. First, the received signals are processed using Fast Fourier Transform(FFT). Then the cross-correlation of every frequency unit is processed by using a pilot signal in frequency domain. The final TDD is obtained by calculating statistically the TDD results of every frequency unit, as TDD of noise frequency unit is random, and TDD of target are nearly consistent. The theoretical analysis and experiment results show that the method is valid and the signal-to-noise ratio tolerance of the method is much better than the cross-correlation of frequency domain method. A reference idea is provided for the time delay difference of weak line spectrum target.