Abstract: A new weight-fusion algorithm was proposed for frequency estimation of the signal with the known frequency-difference and the same length (KFDSL-signal), due to its significant research value and disadvantages of its present frequency estimation methods. In order to make KFDSL-signal spectrum as the same as the spectrum of the signal with the same frequency and length, the frequency-difference amend matrix is given. For the phase-incoherent of KFDSL-signal, the phase compensating matrix is created, which can make phase coherent and noise eliminate. Next, KFDSL-signal spectrum is weight-fused by this matrix to turn almost the same as the spectrum of the phase-coherent sinusoid signal. Consequently, high frequency estimation precision can be obtained through spectral peak searching of the weight-fusion spectrum. Algorithm analyses and simulation results show that this algorithm works quite well in term of precision, calculation, noise immunity, significant theoretical and practical value, and fits for any type of KFDSL-signal.