To suppress the spectrum leakage influence of non-estimated frequency components of a multi-tone signal, a new frequency estimation algorithm was proposed.Firstly, the sampled signal was preprocessed by fast Fourier transform (FFT) algorithm to get the spectrum index of each frequency component, and the coarse estimation values of the amplitude and initial phase of each frequency component were obtained sequentially.Then, the non-estimated frequency components of the multi-tone single were filtered by afrequency shift strategy to obtain a down frequency signal.Finally, the down frequency signal was processed by spectrum analysis, and the more accurate estimation values of frequency, amplitude and initial phase estimates of each frequency component were achieved with an iterative procedure.Moreover, simulation experiments were carried out in different conditions, such as no noise, different signal to noise ratio, etc.The simulation results indicate that the proposed algorithm has a good frequency estimation performanceand improves the frequency estimation accuracy , which effectively suppresses the spectrum leakage influence of the multi-tone signal and is superior to the existing excellent algorithms.