A novel approach to data processing for relay protection is proposed based on analysis of basic requirements of data processing in digital substation.The new scheme involves three major steps，applying the Fourier algorithm immediately to equal-interval sampling data from merging unit，amending the sine/cosine items in accordance with the real-time frequency，and finally acquiring the signals true root mean square value and phase.The new scheme not only obtains high precision frequency with the phase-shift-cycle measurement algorithm，but also adapts to phasor based protection without using interpolation or sampling rate conversion.The concrete implementation of novel data processing approach and related issues（e.g.how to deal with startup with sampled values）are given in detail.The feasibility and validity of proposed approach have been verified with ATP based simulation.