The heterodyne phase measurement using radio frequency (RF) signal can only be performed in a sufficiently high signal-to-noise ratio (SNR). Because the strength of heterodyne signal is extremely sensitive to the phase front misalignment between the signal and the reference beams, the requirement of high SNR greatly limits its implementation. An innovative heterodyne phase measurement method using sequence shifting and genetic algorithm (GA) is reported in this paper. In the method, after being shifted with different steps, the digital sequences of the heterodyne signals containing the phases to be measured are added up. Taking the shifting steps of the sequences as variables, the GA searches the optimal shifting steps, with which the signal strength in the sum can reach the maximum. When the algorithm converges, the phase information can be derived by the optimal shifting steps. Numerical analysis indicates that the root mean square error (RMSE) of the phase measurement by our method can be less than λ/40 even when SNR is as low as −10dB. With the excellent performance in low SNR, the new measurement method can be realized easily in practical applications.