In this work, a solution based on sub-sampling technology for heterodyne signals is proposed. While achieving higher measurement resolution and measurement speed, the performance requirements for the analog-to-digital converter and microprocessor are greatly reduced. The heterodyne signal is a sparse signal with a single frequency at each moment, only its phase offset contains displacement information. We use the pulse counting method to obtain the periods of the signal, and a sampler with a sampling rate well below the frequency of the heterodyne signal. The phase of the sampling point can be restored through sub-sampling technology and extended Kalman filtering. In the experiment, we used 16-bit ADCs with a 600 Ksas sampling rate to sample the heterodyne signals with a center frequency of 10 MHz and the dynamic range from 1 MHz to 19 MHz. The simulation results indicate that our method can effectively calculate the phase information of the interference signal.