In order to improve the velocity measurement accuracy of photoelectric encoder, a velocity measurement method based on the single Moir fringe is introduced. First, Moir fringe photoelectric signals are transported into DSP through a AD acquisition card with EMD(Empirical Mode Decomposition) algorithm which is used to curb DC components. Then, the Hilbert transform is utilized to analyze the change of signal phase and the instantaneous signal frequency calculated by using the difference arithmetic. At last, encoder velocity is derived from the specific parameters of the encoder. Experiment results on certain 21 bit photoelectric encoder indicate that the root mean square of the measurement errors has reduced from 0.022 4 rad/s to 0.013 4 rad/s. This method is of high speed stability, strong anti-interference ability, and can be used for precision speed occasions with higher requirement.