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Aiming at the requirement of fast frequency estimation for high-speed underwater acoustic communication, an improved algorithm for fast frequency estimation with short sequences is proposed based on the algorithm of three-point self-correlation. Increasing a sampling data is adopted for the improved algorithm of fast frequency estimation. The precision of frequency estimation is improved, but the operation amount is almost equal to the ones of the other algorithm. The simulation results show that the Root Mean Square (RMS) of the improved algorithm is closer to Cramer-Rao Bound (CRB) than the ones of the other algorithm. What's more, the RMS of the improved algorithm outperform the ones of the other method by 10dB in the environment with low signal-noise-ratio (SNR), and it is better for the higher frequency signal with the same SNR, and the RMS can reach the CRB while the SNR is increased to 10dB at the condition of 6kHz frequency signal.