In order to accurately extract the phase of the measured object in a vibrating environment, a phase extraction algorithm based on double time domain Fourier transform is proposed. A time domain light intensity signal with two interference periods is divided into several sub-segments with one period. The phase shift frequency introduced by phase shifter and other interference frequencies are separated by carrying out Fourier transform twice. Simulation and experimental results show that the algorithm significantly improves the system’s ability to resist interference under the premise of not improving the system complexity and greatly reducing the data acquisition amount. Compared with the traditional four step phase shift algorithm under the ideal condition, the root mean square error of the measurement can reach 0.062 rad. The proposed method is without manual intervention from acquisition to phase extraction of the measured object, which is conducive to the realization of automation.