The invention discloses a frequency estimation method which comprises the following steps: sampling echo signals of a surface acoustic wave sensor to obtain an information matrix; reconstructing the information matrix to obtain a reconstructed matrix; performing noise reduction processing on the reconstructed matrix to obtain a noise reduction matrix; and performing fast Fourier transform (FFT) onthe noise reduction matrix, and calculating the frequency of the echo signal according to the result of the FFT. According to the invention, an information matrix obtained by echo signal sampling isreconstructed, the reconstruction matrix is subjected to noise reduction processing to obtain the noise reduction matrix. The frequency of the echo signal is estimated by using the FFT algorithm, andthe redundant part of the information is filtered through noise reduction, so that the operand is reduced, the operation speed of the FFT algorithm is improved, the interference of invalid informationis avoided, and the frequency resolution of the FFT algorithm is improved. The invention also discloses a frequency estimation device and system and a computer readable storage medium, which have thesame beneficial effects as the frequency estimation method.