The fast fourier transform (FFT) frequency estimation algorithm combined with the singular value decomposition(SVD) is proposed in this paper,which is used to estimate the frequency of the surface acoustic wave(SAW) resonant sensor.The echo signal of wireless SAW resonator is extracted by the method of repeated sampling. The SVD method is used to remove the white noise in echo signal before FFT,and the Gauss curve fitting method is applied to calibrate the frequency calculated by FFT.The mean square error(MSE) applying the proposed algorithm is 1.53×103,while the MSE directly applying FFT algorithm is 2.38×103，which is reduced by 55%.Thus,using the frequency estimation algorithm combining the SVD and FFT,the accuracy and stability are greatly improved,and the algorithm is simple to operate and easy to implement.