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A novel method based on the analysis of instantaneous phase is proposed to extract the jitter on phase-locked loops output clock. The method utilizes the Hilbert transform to extend the real signal of PLLs output into an analytic signal, and the implementation of Hilbert transform is based on the Fourier transform windowed with Hamming window. Then, the jitter of clock is extracted from the instantaneous phase of analytic signal. The experimental results of simulations validate that the proposed method can effectively extract the jitter on PLL clock, and it has better performance by comparing the sinusoidal jitter extraction results with the other methods.