Abstract: In order to precisely measure the phase difference between two sweeping signals with rapid cycling mode, it is necessary to select a method of signal acquisition and phase difference measurement algorithms for the RF accelerated voltage of the CSNS/RCS (China Spallation Neutron Source/Rapid Cycling Synchrotron) RF system and beam signal. The frequencies of both signals change synchronously. In this paper, measurement algorithms of signals with the same frequency are introduced and the features and applicability of those algorithms are discussed. Secondly, two different FFT spectrum analysis algorithms are elaborated and compared, including FFT cross-spectral method and FFT interpolation method adding cosine window. Then a sweep signal phase difference measurement system is set up using NI virtual instrument technology and Labview graphical programming technology for simulating those algorithms. According to the simulation results, the method of FFT interpolation method adding cosine window can meet the requirements of the fast cycling sweep signal phase difference measurement precision.