Abstract: Sub-sampling technique provides a way of fulfilling fully digital measurement and simplifying the electronic system. In order to reduce the interference brought by sub-sampling and improve traditional sub-sampling digital synchronous demodulation method, the sub-sampling spectrum analysis method was introduced. This method was based on spectrum analysis method under Nyquist sampling, obtained the phase information from low frequency signal after sub-sampling and fulfilled a better performance of anti-jamming. Furthermore, measurement performances under the influence of various interferences were compared between these two methods based on simulation. Data shows that the accuracy of sub-sampling spectrum analysis method was 0.13(0.68 mm at 80 MHz modulation frequency) with 1 MHz measuring speed, under the condition of SNR 40 dB, spurious frequency, frequency deviation 0.1 MHz and second harmonic, this method could performance better than the traditional one. Consequently, sub-sampling spectrum analysis method is applicable to high speed and high accuracy fully digital phase-shift measurement.