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A improved frequency estimation technique is proposed in this paper. The method is based on the frequency estimation algorithm using phase difference of overlap FFT. In overlap FFT, the frequency is obtained by removing the initial phase in the FFT coefficient which is from two discrete sinusoidal sequences of different length. The paper derived the root-mean-square-error (RMSE) formula of the estimation algorithm under Gauss white noise; the formula shows the relationship between the lengths of the two sequences and RMSE. By minimizing RMSE, a better precept about how to choose the length of the second sequence is put forward, so the algorithm is improved. After computer simulation, the effective of modification is proved.