The heterodyne interferometer is widely used as a precise displacement sensor in ultraprecision processing. However, there is a trade-off between measurement speed and measurement precision in the existing interference signal processing methods. In this work, a novel phase measurement method based on digital dual frequency comb is proposed. The proposed method uses the intrinsic frequency comb signal and a narrowband low-pass filter to form a band-pass filter bank, which divides the broadband brought by high-speed movement into multiple narrow bands. The signal-to-noise ratio (SNR) is improved for phase calculation. In addition, two groups of intrinsic frequency comb signals are used simultaneously for phase measurement and the rotation of the output, preventing the inaccurate phase measurement of the input signal whose frequency is the average of two frequencies in the frequency comb signal. The heterodyne laser interferometer can maintain high precision at high measurement speed. The simulation results show that the precision of the proposed method is more than 50% higher than that of the phase-locked loop method. The experiment with a circuit board combined with 100 Msps sampling 16-bit A/D converter shows that the phase measurement precision of the input signal frequency in the bandwidth range of 2.5–37.5 MHz can reach 0.77 mrad, equivalent to the displacement measurement precision of the double-pass interferometer (19 pm) at a measurement speed of less than 2.77 m/s.