In order to effectively reduce the frequency estimation error of single complex sinusoid, aiming at the estimation error of the traditional Rife algorithm caused by the judgment error of the maximum amplitude and sub maximum amplitude spectral line under the condition of low signal-to-noise ratio, replacing the Fast Fourier Transform(FFT) result with frequency estimation result of Root Multiple Signal Classification(RootMUSIC) algorithm is adopted to determine the maximum amplitude and sub maximum amplitude spectral line. In view of the problem that the estimation error of Rife algorithm in some frequency intervals is larger than that in other intervals, frequency shift andre-estimation method is employed to further reduce the estimation error in the whole frequency estimation range. Simulation results show that the proposed RootMUSIC-Modified-Rife(RM-Rife) algorithm has better estimation performance than Rife algorithm, RootMUSIC algorithm and Modified-Rife(M-Rife) algorithm under low SNR conditions, and can be applied to related engineering practice.