In frequency modulated continuous wave (FWCM) measurement system, real-time data processing speed is critical for system responsiveness. At high beat signal frequencies, the vast amount of data acquired significantly increases the time required for fast Fourier transform (FFT) calculations. In this paper, a multi-frequency sampling method based on the Chinese remainder theorem is proposed, which replaces the hardware multi-channel under-sampling by means of software sampling at intervals, realizes the accurate estimation of the frequency of the beat signal, and greatly reduces the calculated data. It has great advantages especially when dealing with high frequency signals. The simulation results prove the feasibility of the method and demonstrate the improvement of the calculation speed of the multi-frequency sampling method.