For high precise frequency estimation of the short sinusoid signal at low signal-to-noise ratio (SNR), a weighted fusion algorithm for frequency estimation of the short signal with the same frequency and length (SFL-Signal) is proposed. The spectrum model of SFL-Signal and the phase compensation matrix with phase coherent and noise cancellation are constructed. Secondly, the SFL-signal spectrum is weight-fused with the phase compensation matrix to obtain the result almost the same as that of the spectrum of the phase-coherent sinusoid signal. Consequently, high frequency estimation precision is obtained with spectral peak searching of the weight-fusion spectrum. Algorithm analysis and simulation results show that, compared with the existing methods,the proposed algorithm works better in term of precision, calculation complexity, noise immunity, and fits for any type of SFL-Signal.